From c05d665f040004fc66efc4d124c993d0b1f3f90b Mon Sep 17 00:00:00 2001 From: abICS Developers Date: Tue, 12 Sep 2023 07:56:12 +0000 Subject: [PATCH] Deploy docs to develop by GitHub Actions triggered by 9568df29468c7f0aab33f33d41e13fbabba19a25 --- .../develop/api/_modules/abics/exception.html | 25 ++++-- .../api/_modules/abics/loggers/loggers.html | 15 ++-- docs/develop/api/_modules/abics/model.html | 32 ++++--- .../api/_modules/abics/replica_params.html | 78 +++++++++++----- docs/develop/api/_modules/index.html | 10 +-- docs/develop/api/_static/basic.css | 22 +++++ .../api/_static/documentation_options.js | 3 +- docs/develop/api/_static/pygments.css | 1 + docs/develop/api/_static/searchtools.js | 26 ++++-- docs/develop/api/_static/sphinx_highlight.js | 16 +++- docs/develop/api/abics.applications.html | 16 ++-- ...tions.latgas_abinitio_interface.aenet.html | 12 +-- ...gas_abinitio_interface.aenet_pylammps.html | 12 +-- ...tgas_abinitio_interface.aenet_trainer.html | 12 +-- ...latgas_abinitio_interface.base_solver.html | 12 +-- ...s_abinitio_interface.default_observer.html | 12 +-- ...ions.latgas_abinitio_interface.defect.html | 12 +-- ...pplications.latgas_abinitio_interface.html | 16 ++-- ...latgas_abinitio_interface.map2perflat.html | 12 +-- ...latgas_abinitio_interface.model_setup.html | 12 +-- ...tgas_abinitio_interface.naive_matcher.html | 12 +-- ...ions.latgas_abinitio_interface.openmx.html | 12 +-- ...ions.latgas_abinitio_interface.params.html | 12 +-- ...ications.latgas_abinitio_interface.qe.html | 12 +-- ...atgas_abinitio_interface.run_base_mpi.html | 12 +-- ...initio_interface.user_function_solver.html | 12 +-- ...ations.latgas_abinitio_interface.vasp.html | 12 +-- .../api/abics.applications.lattice_model.html | 16 ++-- ...bics.applications.lattice_model.potts.html | 12 +-- docs/develop/api/abics.exception.html | 22 ++--- docs/develop/api/abics.html | 18 ++-- docs/develop/api/abics.loggers.html | 18 ++-- docs/develop/api/abics.loggers.loggers.html | 14 +-- docs/develop/api/abics.mc.html | 12 +-- docs/develop/api/abics.mc_mpi.html | 12 +-- docs/develop/api/abics.mlref.html | 12 +-- docs/develop/api/abics.model.html | 24 ++--- docs/develop/api/abics.observer.html | 12 +-- docs/develop/api/abics.replica_params.html | 90 +++++++++---------- docs/develop/api/abics.sampling.html | 16 ++-- docs/develop/api/abics.sampling.mc.html | 12 +-- docs/develop/api/abics.sampling.mc_mpi.html | 12 +-- docs/develop/api/abics.sampling.pamc.html | 12 +-- .../api/abics.sampling.resampling.html | 12 +-- docs/develop/api/abics.sampling.rxmc.html | 12 +-- .../api/abics.sampling.simple_parallel.html | 12 +-- .../api/abics.scripts.abicsRXsepT.html | 12 +-- .../api/abics.scripts.activelearn.html | 12 +-- docs/develop/api/abics.scripts.html | 16 ++-- docs/develop/api/abics.scripts.main.html | 12 +-- .../api/abics.scripts.main_dft_latgas.html | 12 +-- .../develop/api/abics.scripts.main_potts.html | 12 +-- .../develop/api/abics.scripts.mocksolver.html | 12 +-- .../api/abics.scripts.st2abics_config.html | 12 +-- docs/develop/api/abics.scripts.train.html | 12 +-- docs/develop/api/abics.util.html | 12 +-- docs/develop/api/genindex.html | 10 +-- docs/develop/api/index.html | 14 +-- docs/develop/api/modules.html | 12 +-- docs/develop/api/py-modindex.html | 10 +-- docs/develop/api/search.html | 10 +-- docs/develop/api/searchindex.js | 2 +- .../en/html/_sources/about/info.rst.txt | 15 +++- docs/develop/en/html/_static/basic.css | 22 +++++ .../en/html/_static/documentation_options.js | 3 +- docs/develop/en/html/_static/pygments.css | 1 + docs/develop/en/html/_static/searchtools.js | 26 ++++-- .../en/html/_static/sphinx_highlight.js | 16 +++- docs/develop/en/html/about/index.html | 17 ++-- docs/develop/en/html/about/info.html | 36 +++++--- docs/develop/en/html/acknowledge/index.html | 17 ++-- docs/develop/en/html/algorithm/index.html | 25 +++--- docs/develop/en/html/contact/index.html | 17 ++-- docs/develop/en/html/genindex.html | 15 ++-- docs/develop/en/html/how_to_use/index.html | 43 +++++---- docs/develop/en/html/index.html | 19 ++-- docs/develop/en/html/inputfiles/index.html | 17 ++-- .../en/html/inputfiles/parameter_config.html | 25 +++--- .../en/html/inputfiles/parameter_log.html | 21 +++-- .../en/html/inputfiles/parameter_mlref.html | 21 +++-- .../html/inputfiles/parameter_observer.html | 21 +++-- .../html/inputfiles/parameter_sampling.html | 21 +++-- .../en/html/inputfiles/parameter_solver.html | 21 +++-- .../en/html/inputfiles/parameter_train.html | 21 +++-- docs/develop/en/html/install/index.html | 17 ++-- docs/develop/en/html/install/install.html | 29 +++--- docs/develop/en/html/outputfiles/index.html | 37 ++++---- docs/develop/en/html/search.html | 15 ++-- docs/develop/en/html/searchindex.js | 2 +- docs/develop/en/html/tools/index.html | 17 ++-- .../en/html/tools/tools_abicsRXsepT.html | 17 ++-- .../develop/en/html/tools/tools_st2abics.html | 21 +++-- docs/develop/en/html/tutorial/aenet.html | 75 ++++++++-------- docs/develop/en/html/tutorial/index.html | 17 ++-- docs/develop/en/html/tutorial/qe.html | 23 +++-- docs/develop/en/html/tutorial/vasp.html | 23 +++-- .../ja/html/_sources/about/info.rst.txt | 15 ++++ docs/develop/ja/html/_static/basic.css | 22 +++++ .../ja/html/_static/documentation_options.js | 3 +- docs/develop/ja/html/_static/pygments.css | 1 + docs/develop/ja/html/_static/searchtools.js | 26 ++++-- .../ja/html/_static/sphinx_highlight.js | 16 +++- docs/develop/ja/html/_static/translations.js | 3 +- docs/develop/ja/html/about/index.html | 19 ++-- docs/develop/ja/html/about/info.html | 38 +++++--- docs/develop/ja/html/acknowledge/index.html | 19 ++-- docs/develop/ja/html/algorithm/index.html | 27 +++--- docs/develop/ja/html/contact/index.html | 19 ++-- docs/develop/ja/html/genindex.html | 17 ++-- docs/develop/ja/html/how_to_use/index.html | 45 +++++----- docs/develop/ja/html/index.html | 23 +++-- docs/develop/ja/html/inputfiles/index.html | 19 ++-- .../ja/html/inputfiles/parameter_config.html | 27 +++--- .../ja/html/inputfiles/parameter_log.html | 23 +++-- .../ja/html/inputfiles/parameter_mlref.html | 23 +++-- .../html/inputfiles/parameter_observer.html | 23 +++-- .../html/inputfiles/parameter_sampling.html | 23 +++-- .../ja/html/inputfiles/parameter_solver.html | 23 +++-- .../ja/html/inputfiles/parameter_train.html | 23 +++-- docs/develop/ja/html/install/index.html | 19 ++-- docs/develop/ja/html/install/install.html | 31 ++++--- docs/develop/ja/html/outputfiles/index.html | 39 ++++---- docs/develop/ja/html/search.html | 17 ++-- docs/develop/ja/html/searchindex.js | 2 +- docs/develop/ja/html/tools/index.html | 19 ++-- .../ja/html/tools/tools_abicsRXsepT.html | 19 ++-- .../develop/ja/html/tools/tools_st2abics.html | 23 +++-- docs/develop/ja/html/tutorial/aenet.html | 77 ++++++++-------- docs/develop/ja/html/tutorial/index.html | 19 ++-- docs/develop/ja/html/tutorial/qe.html | 25 +++--- docs/develop/ja/html/tutorial/vasp.html | 25 +++--- 131 files changed, 1336 insertions(+), 1161 deletions(-) diff --git a/docs/develop/api/_modules/abics/exception.html b/docs/develop/api/_modules/abics/exception.html index 9a5a5a3b..339bb46b 100644 --- a/docs/develop/api/_modules/abics/exception.html +++ b/docs/develop/api/_modules/abics/exception.html @@ -10,11 +10,11 @@ - - - - - + + + + + @@ -85,12 +85,17 @@

Source code for abics.exception

 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see http://www.gnu.org/licenses/.
 
-
[docs]class Error(Exception):
+

+[docs]
+class Error(Exception):
     """Base class for exceptions in abICS"""
     pass

 
 
-
[docs]class InputError(Error):
+
+

+[docs]
+class InputError(Error):
     """Exception raised for errors in the input
 
     Attributes
@@ -102,7 +107,10 @@ 
Source code for abics.exception
         self.message = message

 
 
-
[docs]class MatrixParseError(Error):
+
+

+[docs]
+class MatrixParseError(Error):
     """Exception raised for matrix parse errors
 
     Attributes
@@ -112,6 +120,7 @@ 
Source code for abics.exception
     """
     def __init__(self, message: str):
         self.message = message

+
diff --git a/docs/develop/api/_modules/abics/loggers/loggers.html b/docs/develop/api/_modules/abics/loggers/loggers.html index 2f2a01e6..bd660a91 100644 --- a/docs/develop/api/_modules/abics/loggers/loggers.html +++ b/docs/develop/api/_modules/abics/loggers/loggers.html @@ -10,11 +10,11 @@ - - - - - + + + + + @@ -212,7 +212,9 @@

Source code for abics.loggers.loggers

         raise NotImplementedError("Unable to do for MPI file handler!")
 
 
-
[docs]def set_log_handles(
+

+[docs]
+def set_log_handles(
     app_name: str,
     level: int = logging.INFO,
     console: str = "default",
@@ -466,6 +468,7 @@ 
Source code for abics.loggers.loggers
             fh.addFilter(_AppFilter(app_name))
             root_log.addHandler(fh)

 
+
     # **********************************************************************************
diff --git a/docs/develop/api/_modules/abics/model.html b/docs/develop/api/_modules/abics/model.html index a887ec5c..c1c7fc32 100644 --- a/docs/develop/api/_modules/abics/model.html +++ b/docs/develop/api/_modules/abics/model.html @@ -10,11 +10,11 @@ - - - - - + + + + + @@ -98,7 +98,9 @@

Source code for abics.model

 """Defines base classes for Monte Carlo simulations"""
 
 
-
[docs]class Model(metaclass=ABCMeta):
+

+[docs]
+class Model(metaclass=ABCMeta):
     """This class defines a model whose energy equals 0 no matter the configuration, and the configuration
     never changes.
     This is a base template for building useful models."""
@@ -107,7 +109,9 @@ 
Source code for abics.model
 
     # def __init__(self):
 
-
[docs]    @abstractmethod
+

+[docs]
+    @abstractmethod
     def energy(self, config) -> float:
         """
         Calculate energy of configuration: input: config
@@ -124,7 +128,10 @@ 
Source code for abics.model
         """
         ...

 
-
[docs]    @abstractmethod
+
+

+[docs]
+    @abstractmethod
     def trialstep(self, config, energy: float) -> tuple[Any, float]:
         """Define a trial step on config
 
@@ -154,7 +161,10 @@ 
Source code for abics.model
         # which can sometimes be costly
         ...

 
-
[docs]    @abstractmethod
+
+

+[docs]
+    @abstractmethod
     def newconfig(self, config, dconfig):
         """
         Update config by using the trial step, dconfig
@@ -172,7 +182,9 @@ 
Source code for abics.model
         config: config object
             updated configuration
         """
-        return config

+        return config

+

+
 
 # For backward compatibility
 if __version__ < "3":
diff --git a/docs/develop/api/_modules/abics/replica_params.html b/docs/develop/api/_modules/abics/replica_params.html
index a0aedd1a..fe130acc 100644
--- a/docs/develop/api/_modules/abics/replica_params.html
+++ b/docs/develop/api/_modules/abics/replica_params.html
@@ -10,11 +10,11 @@
     
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -74,7 +74,9 @@ 
Source code for abics.replica_params
 from typing import Any
 from collections.abc import MutableMapping
 
-
[docs]class SamplerParams:
+

+[docs]
+class SamplerParams:
     """Parameter set for specifying sampling algorithm
 
     Attributes
@@ -86,7 +88,9 @@ 
Source code for abics.replica_params
     def __init__(self) -> None:
         self.sampler = "RXMC"
 
-
[docs]    @classmethod
+

+[docs]
+    @classmethod
     def from_dict(cls, d: MutableMapping[str, Any]) -> "SamplerParams":
         """
         Read information from dictionary
@@ -107,7 +111,10 @@ 
Source code for abics.replica_params
         params.sampler = d.get("sampler", "RXMC")
         return params

 
-
[docs]    @classmethod
+
+

+[docs]
+    @classmethod
     def from_toml(cls, fname: str) -> "SamplerParams":
         """
         Read information from toml file
@@ -124,10 +131,14 @@ 
Source code for abics.replica_params
         """
         import toml
 
-        return cls.from_dict(toml.load(fname))

+        return cls.from_dict(toml.load(fname))

+

+
 
 
-
[docs]class ParallelRandomParams:
+

+[docs]
+class ParallelRandomParams:
     """Parameter set for parallel random sampling
 
     Attributes
@@ -158,7 +169,9 @@ 
Source code for abics.replica_params
         self.reload = False
         self.seed = 0
 
-
[docs]    @classmethod
+

+[docs]
+    @classmethod
     def from_dict(cls, d: MutableMapping[str, Any]) -> "ParallelRandomParams":
         """
         Read information from dictionary
@@ -185,7 +198,10 @@ 
Source code for abics.replica_params
         params.seed = d.get("seed", 0)
         return params

 
-
[docs]    @classmethod
+
+

+[docs]
+    @classmethod
     def from_toml(cls, fname: str) -> "ParallelRandomParams":
         """
         Read information from toml file
@@ -202,10 +218,14 @@ 
Source code for abics.replica_params
         """
         import toml
 
-        return cls.from_dict(toml.load(fname))

+        return cls.from_dict(toml.load(fname))

+

+
 
 
-
[docs]class ParallelMCParams:
+

+[docs]
+class ParallelMCParams:
     """Parameter set for embarrasingly parallel Monte Carlo
 
     Attributes
@@ -242,7 +262,9 @@ 
Source code for abics.replica_params
         self.reload = False
         self.seed = 0
 
-
[docs]    @classmethod
+

+[docs]
+    @classmethod
     def from_dict(cls, d: MutableMapping[str, Any]) -> "ParallelMCParams":
         """
         Read information from dictionary
@@ -271,7 +293,10 @@ 
Source code for abics.replica_params
         params.seed = d.get("seed", 0)
         return params

 
-
[docs]    @classmethod
+
+

+[docs]
+    @classmethod
     def from_toml(cls, fname: str) -> "ParallelMCParams":
         """
         Read information from toml file
@@ -288,10 +313,14 @@ 
Source code for abics.replica_params
         """
         import toml
 
-        return cls.from_dict(toml.load(fname))

+        return cls.from_dict(toml.load(fname))

+

+
 
 
-
[docs]class RXParams:
+

+[docs]
+class RXParams:
     """Parameter set for replica exchange Monte Carlo
 
     Attributes
@@ -331,7 +360,9 @@ 
Source code for abics.replica_params
         self.reload = False
         self.seed = 0
 
-
[docs]    @classmethod
+

+[docs]
+    @classmethod
     def from_dict(cls, d: MutableMapping[str, Any]) -> "RXParams":
         """
         Read information from dictionary
@@ -361,7 +392,10 @@ 
Source code for abics.replica_params
         params.seed = d.get("seed", 0)
         return params

 
-
[docs]    @classmethod
+
+

+[docs]
+    @classmethod
     def from_toml(cls, fname: str) -> "RXParams":
         """
         Read information from toml file
@@ -378,7 +412,9 @@ 
Source code for abics.replica_params
         """
         import toml
 
-        return cls.from_dict(toml.load(fname))

+        return cls.from_dict(toml.load(fname))

+

+
 

 
            

diff --git a/docs/develop/api/_modules/index.html b/docs/develop/api/_modules/index.html
index 6638ee40..880196c9 100644
--- a/docs/develop/api/_modules/index.html
+++ b/docs/develop/api/_modules/index.html
@@ -10,11 +10,11 @@
     
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
diff --git a/docs/develop/api/_static/basic.css b/docs/develop/api/_static/basic.css
index 7577acb1..30fee9d0 100644
--- a/docs/develop/api/_static/basic.css
+++ b/docs/develop/api/_static/basic.css
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {
diff --git a/docs/develop/api/_static/documentation_options.js b/docs/develop/api/_static/documentation_options.js
index b57ae3b8..7e4c114f 100644
--- a/docs/develop/api/_static/documentation_options.js
+++ b/docs/develop/api/_static/documentation_options.js
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
diff --git a/docs/develop/api/_static/pygments.css b/docs/develop/api/_static/pygments.css
index 08bec689..84ab3030 100644
--- a/docs/develop/api/_static/pygments.css
+++ b/docs/develop/api/_static/pygments.css
@@ -17,6 +17,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
 .highlight .gr { color: #E40000 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #008400 } /* Generic.Inserted */
diff --git a/docs/develop/api/_static/searchtools.js b/docs/develop/api/_static/searchtools.js
index 97d56a74..7918c3fa 100644
--- a/docs/develop/api/_static/searchtools.js
+++ b/docs/develop/api/_static/searchtools.js
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**
diff --git a/docs/develop/api/_static/sphinx_highlight.js b/docs/develop/api/_static/sphinx_highlight.js
index aae669d7..8a96c69a 100644
--- a/docs/develop/api/_static/sphinx_highlight.js
+++ b/docs/develop/api/_static/sphinx_highlight.js
@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});
diff --git a/docs/develop/api/abics.applications.html b/docs/develop/api/abics.applications.html
index d7bd8c12..17925b95 100644
--- a/docs/develop/api/abics.applications.html
+++ b/docs/develop/api/abics.applications.html
@@ -11,11 +11,11 @@
     
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
     
@@ -88,9 +88,9 @@
            

              
   

-
abics.applications package

+
abics.applications package

 

-
Subpackages

+
Subpackages

 

 

 

 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet.html
index 9724218c..aa076aaf 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.aenet module

+
abics.applications.latgas_abinitio_interface.aenet module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet_pylammps.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet_pylammps.html
index fcc958e3..ec2e92cf 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet_pylammps.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet_pylammps.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.aenet_pylammps module

+
abics.applications.latgas_abinitio_interface.aenet_pylammps module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet_trainer.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet_trainer.html
index 3bee097a..dfb88ef1 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet_trainer.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.aenet_trainer.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.aenet_trainer module

+
abics.applications.latgas_abinitio_interface.aenet_trainer module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.base_solver.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.base_solver.html
index 7e505ca6..6fff5080 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.base_solver.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.base_solver.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.base_solver module

+
abics.applications.latgas_abinitio_interface.base_solver module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.default_observer.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.default_observer.html
index c0d2d9c0..428faaa3 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.default_observer.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.default_observer.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.default_observer module

+
abics.applications.latgas_abinitio_interface.default_observer module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.defect.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.defect.html
index 645a2de6..13d3b91f 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.defect.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.defect.html
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-
abics.applications.latgas_abinitio_interface.defect module

+
abics.applications.latgas_abinitio_interface.defect module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.html
index f2af946c..c6a735d4 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.html
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@@ -89,9 +89,9 @@
            

              
   

-
abics.applications.latgas_abinitio_interface package

+
abics.applications.latgas_abinitio_interface package

 

-
Submodules

+
Submodules

 

 

 

 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.map2perflat.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.map2perflat.html
index f087fbb7..523b6a8c 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.map2perflat.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.map2perflat.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.map2perflat module

+
abics.applications.latgas_abinitio_interface.map2perflat module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.model_setup.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.model_setup.html
index 1fd13690..aaa69661 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.model_setup.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.model_setup.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.model_setup module

+
abics.applications.latgas_abinitio_interface.model_setup module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.naive_matcher.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.naive_matcher.html
index 2f838ec9..fc770802 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.naive_matcher.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.naive_matcher.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.naive_matcher module

+
abics.applications.latgas_abinitio_interface.naive_matcher module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.openmx.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.openmx.html
index d3245e0a..2068fbdf 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.openmx.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.openmx.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.openmx module

+
abics.applications.latgas_abinitio_interface.openmx module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.params.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.params.html
index 040ad4e3..58d983f2 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.params.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.params.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.params module

+
abics.applications.latgas_abinitio_interface.params module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.qe.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.qe.html
index 95cce620..5af359fd 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.qe.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.qe.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.qe module

+
abics.applications.latgas_abinitio_interface.qe module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.run_base_mpi.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.run_base_mpi.html
index ca541210..e277e59d 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.run_base_mpi.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.run_base_mpi.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.run_base_mpi module

+
abics.applications.latgas_abinitio_interface.run_base_mpi module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.user_function_solver.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.user_function_solver.html
index 23d898a4..af05fc71 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.user_function_solver.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.user_function_solver.html
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.user_function_solver module

+
abics.applications.latgas_abinitio_interface.user_function_solver module

 

 
 
diff --git a/docs/develop/api/abics.applications.latgas_abinitio_interface.vasp.html b/docs/develop/api/abics.applications.latgas_abinitio_interface.vasp.html
index 630a9c8b..228ec86f 100644
--- a/docs/develop/api/abics.applications.latgas_abinitio_interface.vasp.html
+++ b/docs/develop/api/abics.applications.latgas_abinitio_interface.vasp.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.latgas_abinitio_interface.vasp module

+
abics.applications.latgas_abinitio_interface.vasp module

 

 
 
diff --git a/docs/develop/api/abics.applications.lattice_model.html b/docs/develop/api/abics.applications.lattice_model.html
index 56cd323e..2a4b527e 100644
--- a/docs/develop/api/abics.applications.lattice_model.html
+++ b/docs/develop/api/abics.applications.lattice_model.html
@@ -11,11 +11,11 @@
     
   
   
-        
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@@ -89,9 +89,9 @@
            

              
   

-
abics.applications.lattice_model package

+
abics.applications.lattice_model package

 

-
Submodules

+
Submodules

 

 

 

 
diff --git a/docs/develop/api/abics.applications.lattice_model.potts.html b/docs/develop/api/abics.applications.lattice_model.potts.html
index bb7f76d4..806dc09a 100644
--- a/docs/develop/api/abics.applications.lattice_model.potts.html
+++ b/docs/develop/api/abics.applications.lattice_model.potts.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -90,7 +90,7 @@
            

              
   

-
abics.applications.lattice_model.potts module

+
abics.applications.lattice_model.potts module

 

 
 
diff --git a/docs/develop/api/abics.exception.html b/docs/develop/api/abics.exception.html
index 07752f8c..b7c86980 100644
--- a/docs/develop/api/abics.exception.html
+++ b/docs/develop/api/abics.exception.html
@@ -11,11 +11,11 @@
     
   
   
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+        
     
     
     
@@ -93,22 +93,22 @@
            

              
   

-
abics.exception module

+
abics.exception module

 

 

-exception abics.exception.Error[source]

+exception abics.exception.Error[source]
 
Bases: Exception

 
Base class for exceptions in abICS

 

 
 

 

-exception abics.exception.InputError(message: str)[source]

+exception abics.exception.InputError(message: str)[source]
 
Bases: Error

 
Exception raised for errors in the input

 

 

-message

+message
 
explanation

 

 
Type:

@@ -121,12 +121,12 @@
 
 

 

-exception abics.exception.MatrixParseError(message: str)[source]

+exception abics.exception.MatrixParseError(message: str)[source]
 
Bases: Error

 
Exception raised for matrix parse errors

 

 

-message

+message
 
explanation

 

 
Type:

diff --git a/docs/develop/api/abics.html b/docs/develop/api/abics.html
index 20950999..9ab3a0ac 100644
--- a/docs/develop/api/abics.html
+++ b/docs/develop/api/abics.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -93,9 +93,9 @@
            

              
   

-
abics package

+
abics package

 

-
Subpackages

+
Subpackages

 

 

 

 
diff --git a/docs/develop/api/abics.loggers.html b/docs/develop/api/abics.loggers.html
index 400a9981..21012f34 100644
--- a/docs/develop/api/abics.loggers.html
+++ b/docs/develop/api/abics.loggers.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -88,9 +88,9 @@
            

              
   

-
abics.loggers package

+
abics.loggers package

 

-
Submodules

+
Submodules

 

 
    
 
  • abics.loggers.loggers module
      
@@ -101,11 +101,11 @@ 
      Submodules
-
      Module contents
      
+
      Module contents
      
 
      Module taking care of logging duties.
      
 
      
 
      
-abics.loggers.set_log_handles(app_name: str, level: int = 20, console: str = 'default', console_level: int = None, logfile_path: Path | None = None, logfile_mode: str | None = None, logfile_level: int = None, logfile_rank=None, params: dict | None = None)[source]
      
+abics.loggers.set_log_handles(app_name: str, level: int = 20, console: str = 'default', console_level: int = None, logfile_path: Path | None = None, logfile_mode: str | None = None, logfile_level: int = None, logfile_rank=None, params: dict | None = None)[source]
 
      Set desired level for package loggers and add file handlers.
      
 
      
 
      Parameters:
      
diff --git a/docs/develop/api/abics.loggers.loggers.html b/docs/develop/api/abics.loggers.loggers.html
index 8f28ef0e..1ce1f6bf 100644
--- a/docs/develop/api/abics.loggers.loggers.html
+++ b/docs/develop/api/abics.loggers.loggers.html
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@@ -89,11 +89,11 @@
            
      
              
   
      
-
      abics.loggers.loggers module
      
+
      abics.loggers.loggers module
      
 
      Logger initialization for package.
      
 
      
 
      
-abics.loggers.loggers.set_log_handles(app_name: str, level: int = 20, console: str = 'default', console_level: int = None, logfile_path: Path | None = None, logfile_mode: str | None = None, logfile_level: int = None, logfile_rank=None, params: dict | None = None)[source]
      
+abics.loggers.loggers.set_log_handles(app_name: str, level: int = 20, console: str = 'default', console_level: int = None, logfile_path: Path | None = None, logfile_mode: str | None = None, logfile_level: int = None, logfile_rank=None, params: dict | None = None)[source]
 
      Set desired level for package loggers and add file handlers.
      
 
      
 
      Parameters:
      
diff --git a/docs/develop/api/abics.mc.html b/docs/develop/api/abics.mc.html
index d97b690a..0fb7a09c 100644
--- a/docs/develop/api/abics.mc.html
+++ b/docs/develop/api/abics.mc.html
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@@ -88,7 +88,7 @@
            
      
              
   
      
-
      abics.mc module
      
+
      abics.mc module
      
 
      
 
 
diff --git a/docs/develop/api/abics.mc_mpi.html b/docs/develop/api/abics.mc_mpi.html
index 8e6137f1..f7697b26 100644
--- a/docs/develop/api/abics.mc_mpi.html
+++ b/docs/develop/api/abics.mc_mpi.html
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@@ -88,7 +88,7 @@
            
      
              
   
      
-
      abics.mc_mpi module
      
+
      abics.mc_mpi module
      
 
      
 
 
diff --git a/docs/develop/api/abics.mlref.html b/docs/develop/api/abics.mlref.html
index c651cf5c..f02db9b1 100644
--- a/docs/develop/api/abics.mlref.html
+++ b/docs/develop/api/abics.mlref.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -88,7 +88,7 @@
            
      
              
   
      
-
      abics.mlref module
      
+
      abics.mlref module
      
 
      
 
 
diff --git a/docs/develop/api/abics.model.html b/docs/develop/api/abics.model.html
index a3a3b1ac..eb7bec5d 100644
--- a/docs/develop/api/abics.model.html
+++ b/docs/develop/api/abics.model.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -92,17 +92,17 @@
            
      
              
   
      
-
      abics.model module
      
+
      abics.model module
      
 
      
 
      
-class abics.model.Model[source]
      
+class abics.model.Model[source]
 
      Bases: object
      
 
      This class defines a model whose energy equals 0 no matter the configuration, and the configuration
 never changes.
 This is a base template for building useful models.
      
 
      
 
      
-abstract energy(config) → float[source]
      
+abstract energy(config) → float[source]
 
      Calculate energy of configuration: input: config
      
 
      
 
      Parameters:
      
@@ -119,12 +119,12 @@
 
 
      
 
      
-model_name = ''
      
+model_name = ''
 
      
 
 
      
 
      
-abstract newconfig(config, dconfig)[source]
      
+abstract newconfig(config, dconfig)[source]
 
      Update config by using the trial step, dconfig
      
 
      
 
      Parameters:
      
@@ -145,7 +145,7 @@
 
 
      
 
      
-abstract trialstep(config, energy: float) → tuple[Any, float][source]
      
+abstract trialstep(config, energy: float) → tuple[Any, float][source]
 
      Define a trial step on config
      
 
      Returns dconfig, which can contain the minimal information for
 constructing the trial configuration from config to be used in newconfig().
@@ -172,7 +172,7 @@
 
 
      
 
      
-abics.model.model
      
+abics.model.model
 
      alias of Model
      
 
      
 
diff --git a/docs/develop/api/abics.observer.html b/docs/develop/api/abics.observer.html
index 9fe3d00c..ba5c8f57 100644
--- a/docs/develop/api/abics.observer.html
+++ b/docs/develop/api/abics.observer.html
@@ -11,11 +11,11 @@
     
   
   
-        
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@@ -88,7 +88,7 @@
            
      
              
   
      
-
      abics.observer module
      
+
      abics.observer module
      
 
      
 
 
diff --git a/docs/develop/api/abics.replica_params.html b/docs/develop/api/abics.replica_params.html
index d3979d2b..aa03bd66 100644
--- a/docs/develop/api/abics.replica_params.html
+++ b/docs/develop/api/abics.replica_params.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -94,15 +94,15 @@
            
      
              
   
      
-
      abics.replica_params module
      
+
      abics.replica_params module
      
 
      
 
      
-class abics.replica_params.ParallelMCParams[source]
      
+class abics.replica_params.ParallelMCParams[source]
 
      Bases: object
      
 
      Parameter set for embarrasingly parallel Monte Carlo
      
 
      
 
      
-nreplicas
      
+nreplicas
 
      The number of replicas
      
 
      
 
      Type:
      
@@ -113,7 +113,7 @@
 
 
      
 
      
-nprocs_per_replica
      
+nprocs_per_replica
 
      The number of processes which a replica uses
      
 
      
 
      Type:
      
@@ -124,7 +124,7 @@
 
 
      
 
      
-kTstart
      
+kTstart
 
      The lower bound of temperature range
      
 
      
 
      Type:
      
@@ -135,7 +135,7 @@
 
 
      
 
      
-kTend
      
+kTend
 
      The upper bound of temperature range
      
 
      
 
      Type:
      
@@ -146,7 +146,7 @@
 
 
      
 
      
-nsteps
      
+nsteps
 
      The number of MC steps
      
 
      
 
      Type:
      
@@ -157,19 +157,19 @@
 
 
      
 
      
-sample_frequency
      
+sample_frequency
 
      The number of MC steps between measurements observables
      
 
      
 
 
      
 
      
-print_frequency
      
+print_frequency
 
      The number of MC steps between show information
      
 
      
 
 
      
 
      
-reload
      
+reload
 
      Whether to restart simulation or not
      
 
      
 
      Type:
      
@@ -180,7 +180,7 @@
 
 
      
 
      
-seed
      
+seed
 
      The seed of the random number generator
 If 0, some random number is used (e.g., system time or some random noise).
      
 
      
@@ -192,7 +192,7 @@
 
 
      
 
      
-classmethod from_dict(d: MutableMapping[str, Any]) → ParallelMCParams[source]
      
+classmethod from_dict(d: MutableMapping[str, Any]) → ParallelMCParams[source]
 
      Read information from dictionary
      
 
      
 
      Parameters:
      
@@ -209,7 +209,7 @@
 
 
      
 
      
-classmethod from_toml(fname: str) → ParallelMCParams[source]
      
+classmethod from_toml(fname: str) → ParallelMCParams[source]
 
      Read information from toml file
      
 
      
 
      Parameters:
      
@@ -228,12 +228,12 @@
 
 
      
 
      
-class abics.replica_params.ParallelRandomParams[source]
      
+class abics.replica_params.ParallelRandomParams[source]
 
      Bases: object
      
 
      Parameter set for parallel random sampling
      
 
      
 
      
-nreplicas
      
+nreplicas
 
      The number of replicas
      
 
      
 
      Type:
      
@@ -244,7 +244,7 @@
 
 
      
 
      
-nprocs_per_replica
      
+nprocs_per_replica
 
      The number of processes which a replica uses
      
 
      
 
      Type:
      
@@ -255,7 +255,7 @@
 
 
      
 
      
-nsteps
      
+nsteps
 
      The number of MC steps
      
 
      
 
      Type:
      
@@ -266,19 +266,19 @@
 
 
      
 
      
-sample_frequency
      
+sample_frequency
 
      The number of MC steps between measurements observables
      
 
      
 
 
      
 
      
-print_frequency
      
+print_frequency
 
      The number of MC steps between show information
      
 
      
 
 
      
 
      
-reload
      
+reload
 
      Whether to restart simulation or not
      
 
      
 
      Type:
      
@@ -289,7 +289,7 @@
 
 
      
 
      
-seed
      
+seed
 
      The seed of the random number generator
 If 0, some random number is used (e.g., system time or some random noise).
      
 
      
@@ -301,7 +301,7 @@
 
 
      
 
      
-classmethod from_dict(d: MutableMapping[str, Any]) → ParallelRandomParams[source]
      
+classmethod from_dict(d: MutableMapping[str, Any]) → ParallelRandomParams[source]
 
      Read information from dictionary
      
 
      
 
      Parameters:
      
@@ -318,7 +318,7 @@
 
 
      
 
      
-classmethod from_toml(fname: str) → ParallelRandomParams[source]
      
+classmethod from_toml(fname: str) → ParallelRandomParams[source]
 
      Read information from toml file
      
 
      
 
      Parameters:
      
@@ -337,12 +337,12 @@
 
 
      
 
      
-class abics.replica_params.RXParams[source]
      
+class abics.replica_params.RXParams[source]
 
      Bases: object
      
 
      Parameter set for replica exchange Monte Carlo
      
 
      
 
      
-nreplicas
      
+nreplicas
 
      The number of replicas
      
 
      
 
      Type:
      
@@ -353,7 +353,7 @@
 
 
      
 
      
-nprocs_per_replica
      
+nprocs_per_replica
 
      The number of processes which a replica uses
      
 
      
 
      Type:
      
@@ -364,7 +364,7 @@
 
 
      
 
      
-kTstart
      
+kTstart
 
      The lower bound of temperature range
      
 
      
 
      Type:
      
@@ -375,7 +375,7 @@
 
 
      
 
      
-kTend
      
+kTend
 
      The upper bound of temperature range
      
 
      
 
      Type:
      
@@ -386,7 +386,7 @@
 
 
      
 
      
-nsteps
      
+nsteps
 
      The number of MC steps
      
 
      
 
      Type:
      
@@ -397,25 +397,25 @@
 
 
      
 
      
-RXtrial_frequency
      
+RXtrial_frequency
 
      The number of MC steps between replica exchange operations
      
 
      
 
 
      
 
      
-sample_frequency
      
+sample_frequency
 
      The number of MC steps between measurements observables
      
 
      
 
 
      
 
      
-print_frequency
      
+print_frequency
 
      The number of MC steps between show information
      
 
      
 
 
      
 
      
-reload
      
+reload
 
      Whether to restart simulation or not
      
 
      
 
      Type:
      
@@ -426,7 +426,7 @@
 
 
      
 
      
-seed
      
+seed
 
      The seed of the random number generator
 If 0, some random number is used (e.g., system time or some random noise).
      
 
      
@@ -438,7 +438,7 @@
 
 
      
 
      
-classmethod from_dict(d: MutableMapping[str, Any]) → RXParams[source]
      
+classmethod from_dict(d: MutableMapping[str, Any]) → RXParams[source]
 
      Read information from dictionary
      
 
      
 
      Parameters:
      
@@ -455,7 +455,7 @@
 
 
      
 
      
-classmethod from_toml(fname: str) → RXParams[source]
      
+classmethod from_toml(fname: str) → RXParams[source]
 
      Read information from toml file
      
 
      
 
      Parameters:
      
@@ -474,12 +474,12 @@
 
 
      
 
      
-class abics.replica_params.SamplerParams[source]
      
+class abics.replica_params.SamplerParams[source]
 
      Bases: object
      
 
      Parameter set for specifying sampling algorithm
      
 
      
 
      
-sampler
      
+sampler
 
      Sampler name
      
 
      
 
      Type:
      
@@ -490,7 +490,7 @@
 
 
      
 
      
-classmethod from_dict(d: MutableMapping[str, Any]) → SamplerParams[source]
      
+classmethod from_dict(d: MutableMapping[str, Any]) → SamplerParams[source]
 
      Read information from dictionary
      
 
      
 
      Parameters:
      
@@ -507,7 +507,7 @@
 
 
      
 
      
-classmethod from_toml(fname: str) → SamplerParams[source]
      
+classmethod from_toml(fname: str) → SamplerParams[source]
 
      Read information from toml file
      
 
      
 
      Parameters:
      
diff --git a/docs/develop/api/abics.sampling.html b/docs/develop/api/abics.sampling.html
index b5a4bff6..16371853 100644
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+++ b/docs/develop/api/abics.sampling.html
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@@ -88,9 +88,9 @@
            
      
              
   
      
-
      abics.sampling package
      
+
      abics.sampling package
      
 
      
-
      Submodules
      
+
      Submodules
      
 
      
 
      
 
      
 
diff --git a/docs/develop/api/abics.sampling.mc.html b/docs/develop/api/abics.sampling.mc.html
index 6e820993..e7e24b4d 100644
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-
      abics.sampling.mc module
      
+
      abics.sampling.mc module
      
 
      
 
 
diff --git a/docs/develop/api/abics.sampling.mc_mpi.html b/docs/develop/api/abics.sampling.mc_mpi.html
index c5d93f78..240fbd52 100644
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-
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+
      abics.sampling.mc_mpi module
      
 
      
 
 
diff --git a/docs/develop/api/abics.sampling.pamc.html b/docs/develop/api/abics.sampling.pamc.html
index 5e000ac9..0f446af6 100644
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-
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+
      abics.sampling.pamc module
      
 
      
 
 
diff --git a/docs/develop/api/abics.sampling.resampling.html b/docs/develop/api/abics.sampling.resampling.html
index ec212dc9..8c1b9e7e 100644
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+
      abics.sampling.resampling module
      
 
      
 
 
diff --git a/docs/develop/api/abics.sampling.rxmc.html b/docs/develop/api/abics.sampling.rxmc.html
index 00c7513f..eea70331 100644
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-
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+
      abics.sampling.rxmc module
      
 
      
 
 
diff --git a/docs/develop/api/abics.sampling.simple_parallel.html b/docs/develop/api/abics.sampling.simple_parallel.html
index 2df5f986..c7f03f96 100644
--- a/docs/develop/api/abics.sampling.simple_parallel.html
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-
      abics.sampling.simple_parallel module
      
+
      abics.sampling.simple_parallel module
      
 
      
 
 
diff --git a/docs/develop/api/abics.scripts.abicsRXsepT.html b/docs/develop/api/abics.scripts.abicsRXsepT.html
index 0be69b2e..25eca4c2 100644
--- a/docs/develop/api/abics.scripts.abicsRXsepT.html
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+
      abics.scripts.abicsRXsepT module
      
 
      
 
 
diff --git a/docs/develop/api/abics.scripts.activelearn.html b/docs/develop/api/abics.scripts.activelearn.html
index 8cf2f376..dc5654db 100644
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-
      abics.scripts.activelearn module
      
+
      abics.scripts.activelearn module
      
 
      
 
 
diff --git a/docs/develop/api/abics.scripts.html b/docs/develop/api/abics.scripts.html
index ec678b05..165b5fbe 100644
--- a/docs/develop/api/abics.scripts.html
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-
      abics.scripts package
      
+
      abics.scripts package
      
 
      
-
      Submodules
      
+
      Submodules
      
 
      
 
      
 
      
 
diff --git a/docs/develop/api/abics.scripts.main.html b/docs/develop/api/abics.scripts.main.html
index b4912bd8..d746e2a3 100644
--- a/docs/develop/api/abics.scripts.main.html
+++ b/docs/develop/api/abics.scripts.main.html
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-
      abics.scripts.main module
      
+
      abics.scripts.main module
      
 
      
 
 
diff --git a/docs/develop/api/abics.scripts.main_dft_latgas.html b/docs/develop/api/abics.scripts.main_dft_latgas.html
index 9e0e4e40..ce29ef07 100644
--- a/docs/develop/api/abics.scripts.main_dft_latgas.html
+++ b/docs/develop/api/abics.scripts.main_dft_latgas.html
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-
      abics.scripts.main_dft_latgas module
      
+
      abics.scripts.main_dft_latgas module
      
 
      
 
 
diff --git a/docs/develop/api/abics.scripts.main_potts.html b/docs/develop/api/abics.scripts.main_potts.html
index 0378f058..316195c1 100644
--- a/docs/develop/api/abics.scripts.main_potts.html
+++ b/docs/develop/api/abics.scripts.main_potts.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -89,7 +89,7 @@
            
      
              
   
      
-
      abics.scripts.main_potts module
      
+
      abics.scripts.main_potts module
      
 
      
 
 
diff --git a/docs/develop/api/abics.scripts.mocksolver.html b/docs/develop/api/abics.scripts.mocksolver.html
index e6d66a3a..1a03bcd2 100644
--- a/docs/develop/api/abics.scripts.mocksolver.html
+++ b/docs/develop/api/abics.scripts.mocksolver.html
@@ -11,11 +11,11 @@
     
   
   
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-
      abics.scripts.mocksolver module
      
+
      abics.scripts.mocksolver module
      
 
      
 
 
diff --git a/docs/develop/api/abics.scripts.st2abics_config.html b/docs/develop/api/abics.scripts.st2abics_config.html
index 8b6fb627..61d036a8 100644
--- a/docs/develop/api/abics.scripts.st2abics_config.html
+++ b/docs/develop/api/abics.scripts.st2abics_config.html
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-
      abics.scripts.st2abics_config module
      
+
      abics.scripts.st2abics_config module
      
 
      
 
 
diff --git a/docs/develop/api/abics.scripts.train.html b/docs/develop/api/abics.scripts.train.html
index a5657d72..d8d15de9 100644
--- a/docs/develop/api/abics.scripts.train.html
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-
      abics.scripts.train module
      
+
      abics.scripts.train module
      
 
      
 
 
diff --git a/docs/develop/api/abics.util.html b/docs/develop/api/abics.util.html
index be238817..c8b4d028 100644
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-
      abics.util module
      
+
      abics.util module
      
 
      
 
 
diff --git a/docs/develop/api/genindex.html b/docs/develop/api/genindex.html
index 3e0f73cb..5b2a1e2c 100644
--- a/docs/develop/api/genindex.html
+++ b/docs/develop/api/genindex.html
@@ -10,11 +10,11 @@
     
   
   
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diff --git a/docs/develop/api/index.html b/docs/develop/api/index.html
index f1155974..de4e770a 100644
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+++ b/docs/develop/api/index.html
@@ -11,11 +11,11 @@
     
   
   
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@@ -71,7 +71,7 @@
            
      
              
   
      
-
      Welcome to abics’s API documentation!
      
+
      Welcome to abics’s API documentation!
      
 
      
 
      Contents:
      
 
        
@@ -132,7 +132,7 @@ 
        Welcome to abics’s API documentation!
-
        Indices and tables
        
+
        Indices and tables
        
 
          
 
        • Index
          • 
 
        • Module Index
          • 
diff --git a/docs/develop/api/modules.html b/docs/develop/api/modules.html
index 7aa96708..f5821968 100644
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@@ -70,7 +70,7 @@
            
          
              
   
          
-
          abics
          
+
          abics
          
 
          
 
            
 
          • abics package
              
diff --git a/docs/develop/api/py-modindex.html b/docs/develop/api/py-modindex.html
index ec75cd40..163f3435 100644
--- a/docs/develop/api/py-modindex.html
+++ b/docs/develop/api/py-modindex.html
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diff --git a/docs/develop/api/search.html b/docs/develop/api/search.html
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+++ b/docs/develop/api/search.html
@@ -11,11 +11,11 @@
     
   
   
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diff --git a/docs/develop/api/searchindex.js b/docs/develop/api/searchindex.js
index 261c20d2..e6d515b4 100644
--- a/docs/develop/api/searchindex.js
+++ b/docs/develop/api/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["abics", "abics.applications", "abics.applications.latgas_abinitio_interface", "abics.applications.latgas_abinitio_interface.aenet", "abics.applications.latgas_abinitio_interface.aenet_pylammps", "abics.applications.latgas_abinitio_interface.aenet_trainer", "abics.applications.latgas_abinitio_interface.base_solver", "abics.applications.latgas_abinitio_interface.default_observer", "abics.applications.latgas_abinitio_interface.defect", "abics.applications.latgas_abinitio_interface.map2perflat", "abics.applications.latgas_abinitio_interface.model_setup", "abics.applications.latgas_abinitio_interface.naive_matcher", "abics.applications.latgas_abinitio_interface.openmx", "abics.applications.latgas_abinitio_interface.params", "abics.applications.latgas_abinitio_interface.qe", "abics.applications.latgas_abinitio_interface.run_base_mpi", "abics.applications.latgas_abinitio_interface.user_function_solver", "abics.applications.latgas_abinitio_interface.vasp", 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\ No newline at end of file
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"module-abics.loggers.loggers"]], "abics.mc module": [[23, "abics-mc-module"]], "abics.mc_mpi module": [[24, "abics-mc-mpi-module"]], "abics.mlref module": [[25, "abics-mlref-module"]], "abics.model module": [[26, "module-abics.model"]], "abics.observer module": [[27, "abics-observer-module"]], "abics.replica_params module": [[28, "module-abics.replica_params"]], "abics.sampling package": [[29, "abics-sampling-package"]], "abics.sampling.mc module": [[30, "abics-sampling-mc-module"]], "abics.sampling.mc_mpi module": [[31, "abics-sampling-mc-mpi-module"]], "abics.sampling.pamc module": [[32, "abics-sampling-pamc-module"]], "abics.sampling.resampling module": [[33, "abics-sampling-resampling-module"]], "abics.sampling.rxmc module": [[34, "abics-sampling-rxmc-module"]], "abics.sampling.simple_parallel module": [[35, "abics-sampling-simple-parallel-module"]], "abics.scripts package": [[36, "abics-scripts-package"]], "abics.scripts.abicsRXsepT module": [[37, "abics-scripts-abicsrxsept-module"]], "abics.scripts.activelearn module": [[38, "abics-scripts-activelearn-module"]], "abics.scripts.main module": [[39, "abics-scripts-main-module"]], "abics.scripts.main_dft_latgas module": [[40, "abics-scripts-main-dft-latgas-module"]], "abics.scripts.main_potts module": [[41, "abics-scripts-main-potts-module"]], "abics.scripts.mocksolver module": [[42, "abics-scripts-mocksolver-module"]], "abics.scripts.st2abics_config module": [[43, "abics-scripts-st2abics-config-module"]], "abics.scripts.train module": [[44, "abics-scripts-train-module"]], "abics.util module": [[45, "abics-util-module"]], "Welcome to abics\u2019s API documentation!": [[46, "welcome-to-abics-s-api-documentation"]], "Contents:": [[46, null]], "Indices and tables": [[46, "indices-and-tables"]], "abics": [[47, "abics"]]}, "indexentries": {"abics": [[0, "module-abics"]], "module": [[0, "module-abics"], [1, "module-abics.applications"], [18, "module-abics.applications.lattice_model"], 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"abics.replica_params.SamplerParams.sampler"]], "seed (abics.replica_params.parallelmcparams attribute)": [[28, "abics.replica_params.ParallelMCParams.seed"]], "seed (abics.replica_params.parallelrandomparams attribute)": [[28, "abics.replica_params.ParallelRandomParams.seed"]], "seed (abics.replica_params.rxparams attribute)": [[28, "abics.replica_params.RXParams.seed"]], "abics.sampling": [[29, "module-abics.sampling"]], "abics.scripts": [[36, "module-abics.scripts"]]}})
\ No newline at end of file
diff --git a/docs/develop/en/html/_sources/about/info.rst.txt b/docs/develop/en/html/_sources/about/info.rst.txt
index e8f29009..e480cb01 100644
--- a/docs/develop/en/html/_sources/about/info.rst.txt
+++ b/docs/develop/en/html/_sources/about/info.rst.txt
@@ -51,6 +51,20 @@ License
 
 This package is distributed under GNU General Public License version 3 (GPL v3) or later.
 
+We hope that you cite the following article when you publish the results using abICS.
+
+Shusuke Kasamatsu, Yuichi Motoyama, Kazuyoshi Yoshimi, Tatsumi Aoyama, “Configuration sampling in multi-component multi-sublattice systems enabled by ab Initio Configuration Sampling Toolkit (abICS)”, `arXiv:2309.04769 `_.
+
+Bibtex:
+
+@misc{kasamatsu2023configuration,
+title={Configuration sampling in multi-component multi-sublattice systems enabled by ab Initio Configuration Sampling Toolkit (abICS)},
+author={Shusuke Kasamatsu and Yuichi Motoyama and Kazuyoshi Yoshimi and Tatsumi Aoyama},
+year={2023},
+eprint={2309.04769},
+archivePrefix={arXiv},
+primaryClass={cond-mat.mtrl-sci}
+}
 
 Copyright
 --------------
@@ -58,4 +72,3 @@ Copyright
 *(c) 2019- The University of Tokyo. All rights reserved.*
 
 This software was developed with the support of \"*Project for advancement of software usability in materials science*\" of The Institute for Solid State Physics, The University of Tokyo. 
-     
diff --git a/docs/develop/en/html/_static/basic.css b/docs/develop/en/html/_static/basic.css
index 7577acb1..30fee9d0 100644
--- a/docs/develop/en/html/_static/basic.css
+++ b/docs/develop/en/html/_static/basic.css
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {
diff --git a/docs/develop/en/html/_static/documentation_options.js b/docs/develop/en/html/_static/documentation_options.js
index ddf8480e..32144d7b 100644
--- a/docs/develop/en/html/_static/documentation_options.js
+++ b/docs/develop/en/html/_static/documentation_options.js
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '2.1-dev',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
diff --git a/docs/develop/en/html/_static/pygments.css b/docs/develop/en/html/_static/pygments.css
index 691aeb82..0d49244e 100644
--- a/docs/develop/en/html/_static/pygments.css
+++ b/docs/develop/en/html/_static/pygments.css
@@ -17,6 +17,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
 .highlight .gr { color: #FF0000 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */
diff --git a/docs/develop/en/html/_static/searchtools.js b/docs/develop/en/html/_static/searchtools.js
index 97d56a74..7918c3fa 100644
--- a/docs/develop/en/html/_static/searchtools.js
+++ b/docs/develop/en/html/_static/searchtools.js
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**
diff --git a/docs/develop/en/html/_static/sphinx_highlight.js b/docs/develop/en/html/_static/sphinx_highlight.js
index aae669d7..8a96c69a 100644
--- a/docs/develop/en/html/_static/sphinx_highlight.js
+++ b/docs/develop/en/html/_static/sphinx_highlight.js
@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});
diff --git a/docs/develop/en/html/about/index.html b/docs/develop/en/html/about/index.html
index 0b418ed3..316d852e 100644
--- a/docs/develop/en/html/about/index.html
+++ b/docs/develop/en/html/about/index.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     1. About abICS — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
     
@@ -33,7 +32,7 @@
           
              
             
   
              
-
              1. About abICS
              
+
              1. About abICS
              
 
              
 
                
 
              • 1.1. What is abICS ?
                • 
@@ -118,7 +117,7 @@ 
                Quick search
                
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/about/info.html b/docs/develop/en/html/about/info.html
index d7ec45f4..1d793abd 100644
--- a/docs/develop/en/html/about/info.html
+++ b/docs/develop/en/html/about/info.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     1.1. What is abICS ? — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
     
@@ -33,7 +32,7 @@
           
                
             
   
                
-
                1.1. What is abICS ?
                
+
                1.1. What is abICS ?
                
 
                abICS is a software framework for training a machine learning model to
 reproduce first-principles energies and then using the model to perform
 configurational sampling in disordered systems.
@@ -45,7 +44,7 @@ 
                1.1. What is abICS ?
-
                1.2. Developers
                
+
                1.2. Developers
                
 
                abICS is developed by the following members.
                
 
                  
 
                • 
@@ -74,7 +73,7 @@ 
                  1.2. Developers
 
                
 
                
-
                1.3. Version information
                
+
                1.3. Version information
                
 
                  
 
                • ver. 2.1.0    : 2023/06/12.
                  • 
 
                • ver. 2.0.1    : 2022/11/04.
                  • 
@@ -85,11 +84,22 @@ 
                  1.3. Version information
-
                  1.4. License
                  
+
                  1.4. License
                  
 
                  This package is distributed under GNU General Public License version 3 (GPL v3) or later.
                  
+
                  We hope that you cite the following article when you publish the results using abICS.
                  
+
                  Shusuke Kasamatsu, Yuichi Motoyama, Kazuyoshi Yoshimi, Tatsumi Aoyama, “Configuration sampling in multi-component multi-sublattice systems enabled by ab Initio Configuration Sampling Toolkit (abICS)”, arXiv:2309.04769.
                  
+
                  Bibtex:
                  
+
                  @misc{kasamatsu2023configuration,
+title={Configuration sampling in multi-component multi-sublattice systems enabled by ab Initio Configuration Sampling Toolkit (abICS)},
+author={Shusuke Kasamatsu and Yuichi Motoyama and Kazuyoshi Yoshimi and Tatsumi Aoyama},
+year={2023},
+eprint={2309.04769},
+archivePrefix={arXiv},
+primaryClass={cond-mat.mtrl-sci}
+}
                  
 
                
 
@@ -169,7 +179,7 @@ 
                Quick search
                
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/acknowledge/index.html b/docs/develop/en/html/acknowledge/index.html
index 18b2933b..4972797b 100644
--- a/docs/develop/en/html/acknowledge/index.html
+++ b/docs/develop/en/html/acknowledge/index.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     9. Acknowledgement — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
     
@@ -33,7 +32,7 @@
           
                
             
   
                
-
                9. Acknowledgement
                
+
                9. Acknowledgement
                
 
                The development of this software has been supported by various funding bodies and computer resource providers over the years.
                
 
                  
 
                • Priority Issue on Post-K computer (Development of new fundamental technologies for high-efficiency energy creation, conversion/storage and use)
                  • 
@@ -112,7 +111,7 @@ 
                  Quick search
                  
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/algorithm/index.html b/docs/develop/en/html/algorithm/index.html
index 003fbff7..5cf79115 100644
--- a/docs/develop/en/html/algorithm/index.html
+++ b/docs/develop/en/html/algorithm/index.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     8. Algorithm — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
     
@@ -34,7 +33,7 @@
           
                  
             
   
                  
-
                  8. Algorithm
                  
+
                  8. Algorithm
                  
 
                  abICS is designed for combining parallel extended ensemble methods with
 arbitrary energy calculators. At present,
 the replica exchange Monte Carlo method and
@@ -48,7 +47,7 @@ 
                  8. Algorithm
-
                  8.1. Replica exchange Monte Carlo method
                  
+
                  8.1. Replica exchange Monte Carlo method
                  
 
                  A disadvantage of the widely-used Metropolis Monte Carlo algorithm is
 that it tends to get stuck in local minima.
 The replica exchange approach aims to overcome this problem by
@@ -84,7 +83,7 @@ 
                  8.1. Replica exchange Monte Carlo method
 
                
 
                
 
                
-
                8.2. Population Annealing Monte Carlo
                
+
                8.2. Population Annealing Monte Carlo
                
 
                The simulated annealing (SA) method is one of the Monte Carlo method for searching for the ground state.
 SA performs an ordinally MC sampling under a fixed temperature, and decreases temperature after a given number of MC steps finished.
 SA first searches a whole space, and then searches narrower regions gradually as temperature decreases.
@@ -108,7 +107,7 @@ 
                8.2. Population Annealing Monte Carlo
 
                
 
                
-
                8.3. About configuration and update
                
+
                8.3. About configuration and update
                
 
                Here, the outline of the definition of the configuration in abICS and the update by the Monte Carlo method are explained using Fig. 8.1 as an example.
                
 
                (a)-(c) are schematic figures of unitcell, base_structure, and defect_structure, where blue, green, and black circles are the atomic types defined by base_structure, respectively. The star symbol indicates the location of the defects defined by defect_structure.
 (d) is a schematic figure for specifying the atomic species in base_structure. Here, three atomic species of blue, green, and black are defined. How each atom is arranged is defined by coords for each atom type.
@@ -124,7 +123,7 @@ 
                8.3. About configuration and update
 ../_images/alg_sampling.png
 
                
-
                Fig. 8.1 (a)-(e) Definition of lattice in abICS. (f) A schematic of MonteCarlo method. Details are described in the text.
                
+
                Fig. 8.1 (a)-(e) Definition of lattice in abICS. (f) A schematic of MonteCarlo method. Details are described in the text.
                
 
                
 
 
                
@@ -201,7 +200,7 @@ 
                Quick search
                
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/contact/index.html b/docs/develop/en/html/contact/index.html
index 3e913453..3a24d71d 100644
--- a/docs/develop/en/html/contact/index.html
+++ b/docs/develop/en/html/contact/index.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     10. Contacts — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
     
@@ -32,7 +31,7 @@
           
                
             
   
                
-
                10. Contacts
                
+
                10. Contacts
                
 
                  
 
                • About Bugs
                  
 
                  Please report all problems and bugs on the GitHub Issues page
                  
@@ -119,7 +118,7 @@ 
                  Quick search
                  
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/genindex.html b/docs/develop/en/html/genindex.html
index e6a3bc02..1fb5f155 100644
--- a/docs/develop/en/html/genindex.html
+++ b/docs/develop/en/html/genindex.html
@@ -1,16 +1,15 @@
-
 
 
-
+
   
     
     
     Index — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
    
@@ -100,7 +99,7 @@ 
                  Quick search
                  
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
     
                
diff --git a/docs/develop/en/html/how_to_use/index.html b/docs/develop/en/html/how_to_use/index.html
index bd91457b..4d2abba9 100644
--- a/docs/develop/en/html/how_to_use/index.html
+++ b/docs/develop/en/html/how_to_use/index.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     3. Basic Usage — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
     
@@ -34,9 +33,9 @@
           
                
             
   
                
-
                3. Basic Usage
                
+
                3. Basic Usage
                
 
                
-
                3.1. Active learning
                
+
                3.1. Active learning
                
 
                abICS was originally developed for directly combining first-principles calculations with replica-exchange Monte Carlo methods to perform configurational sampling,
 but the scale of the models and the number of steps that can be calculated are limited by the large computational cost of first-principles calculations.
 In contrast, Ver. 2 implements an active learning method to construct a neural network model that can rapidly predict the energy after structural optimization,
@@ -53,7 +52,7 @@ 
                3.1. Active learning
-
                3.2. Preparing an abICS control file
                
+
                3.2. Preparing an abICS control file
                
 
                First, we have to prepare an input file that controls the entire abICS framework.
 The input file of abICS is comprised of the following five sections:
                
 
                  
@@ -191,7 +190,7 @@ 
                  3.1. Active learning
-
                  3.3. Preparing a reference file for first-principles solvers
                  
+
                  3.3. Preparing a reference file for first-principles solvers
                  
 
                  The user must prepare reference input file(s) for first-principles solvers that are used for
 generating the training data according to the input format of the solver.
 The path of the reference file is specified by base_input_dir in the [mlref.solver] section in the abICS input file (see below).
@@ -228,7 +227,7 @@ 
                  3.3. Preparing a reference file for firs
 

 

 

-
3.3.1. Specific notes for first-principles solvers

+
3.3.1. Specific notes for first-principles solvers

 
Every setting other than those pertaining to the atomic coordinates should be set in the solver
 reference input file.
 However, the specification of atoms to be relaxed can be controlled by abICS.
@@ -236,7 +235,7 @@ 
3.3. Preparing a reference file for firs
 Furthermore, to interoperate with abICS, there are a few rules regarding the file name and contents
 of the reference file for each solver. We’ll explain them below.

 

-
VASP

+
VASP

 
 

 

-
Quantum Espresso

+
Quantum Espresso

 

 

-
3.4. Preparing a reference file for training and evaluating the machine learning model

+
3.4. Preparing a reference file for training and evaluating the machine learning model

 
The user must prepare a reference file according to the input format of the
 machine learning model trainer and calculator to be used (only aenet is supported at the moment).
 The path of the reference file is specified by base_input_dir in the [solver] section in the abICS input file (see below).
@@ -293,9 +292,9 @@ 
3.4. Preparing a reference file for trai
 The lattice sites are specified in a separate abICS input file (see below),
 and abICS will take care of generating the coordinates section at each sampling step.

 

-
3.4.1. Machine learning trainer/calculator-specific notes

+
3.4.1. Machine learning trainer/calculator-specific notes

 

-
aenet

+
aenet

 

 

 

-
3.5. Creating a set of training data

+
3.5. Creating a set of training data

 
    
 
  1. Generate a set of input files for the first-principle calculation using abics_mlref.
    2. 
 
  2. Perform the first-principle calculation with these inputs. (In the tutorial GNU parallel is used for the high-throughput calculation.)
    3. 
 

 

 

-
3.6. Creating a neural network

+
3.6. Creating a neural network

 
    
 
  1. Run abics_mlref again to convert the results of the first-principle calculation into a common format that abics_train will read.
    2. 
 
  2. Execute abics_train to create a neural network. When the calculation is completed successfully, the trained neural network is output in baseinput directory.
    3. 
 

 

 

-
3.7. Monte Carlo sampling

+
3.7. Monte Carlo sampling

 
By using abics_sampling, Monte Carlo sampling can be performed by using the trained neural network.
 (The number of MPI processes must be larger than the number of replicas.)
 Running the program will create directories named by the replica numbers under the current directory,
@@ -423,7 +422,7 @@ 
Quick search

       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/index.html b/docs/develop/en/html/index.html
index 7b495a47..b223e796 100644
--- a/docs/develop/en/html/index.html
+++ b/docs/develop/en/html/index.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     Welcome to abICS’s documentation! — abICS 2.1-dev documentation
-    
-    
-    
-    
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+    
+    
+    
+    
+    
     
     
     
@@ -32,7 +31,7 @@
           

             
   

-
Welcome to abICS’s documentation!

+
Welcome to abICS’s documentation!

 

 
Contents:

 
    
@@ -106,7 +105,7 @@ 
    Welcome to abICS’s documentation!
-
    Indices and tables
    
+
    Indices and tables
    
 
      
 
    • Index
      • 
 
    • Module Index
      • 
@@ -179,7 +178,7 @@ 
      Quick search
      
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/inputfiles/index.html b/docs/develop/en/html/inputfiles/index.html
index 0b6df4a7..62518f9e 100644
--- a/docs/develop/en/html/inputfiles/index.html
+++ b/docs/develop/en/html/inputfiles/index.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     5. Input Files Format — abICS 2.1-dev documentation
-    
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+    
+    
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+    
+    
     
     
     
@@ -33,7 +32,7 @@
           
      
             
   
      
-
      5. Input Files Format
      
+
      5. Input Files Format
      
 
      The input file of abICS is constructed by the following five sections:
      
 
        
 
      1. [sampling] section specifies the parameters of the replica exchange Monte Carlo part, such as the number of replicas, the temperature range, and the number of Monte Carlo steps. In addition, [sampling.solver] subsection specifies the parameters for the (first principle calculation) solver, including the type of solver (VASP, QE,…), the path to the solver, and the directory containing immutable input files.
        2. 
@@ -132,7 +131,7 @@ 
        Quick search
        
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/inputfiles/parameter_config.html b/docs/develop/en/html/inputfiles/parameter_config.html
index 14403687..b14bda29 100644
--- a/docs/develop/en/html/inputfiles/parameter_config.html
+++ b/docs/develop/en/html/inputfiles/parameter_config.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     5.6. [config] section — abICS 2.1-dev documentation
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@@ -34,7 +33,7 @@
           
        
             
   
        
-
        5.6. [config] section
        
+
        5.6. [config] section
        
 
        This section specifies configurations such as alloy coordination.
 An example is shown as follows:
        
 
        
@@ -74,14 +73,14 @@
 
        
 
      
 
      
-
      5.6.1. Input Format
      
+
      5.6.1. Input Format
      
 
      Keywords and their values are specified by a keyword and its value in the form keyword = value.
 Comments can also be entered by adding # (Subsequent characters are ignored).
      
 
      
 
      
-
      5.6.2. Key words
      
+
      5.6.2. Key words
      
 
      
-
      In the case of solver.type != "potts"
      
+
      In the case of solver.type != "potts"
      
 
        
 
      • Specify lattice
        
 
        
@@ -267,7 +266,7 @@ 
        In the case of 
 
      
 
      
 
      
-
      In the case of solver.type = "potts"
      
+
      In the case of solver.type = "potts"
      
 
      
 
        
 
      • Q
        
@@ -361,7 +360,7 @@ 
        Quick search
        
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/inputfiles/parameter_log.html b/docs/develop/en/html/inputfiles/parameter_log.html
index 791862f6..2488a885 100644
--- a/docs/develop/en/html/inputfiles/parameter_log.html
+++ b/docs/develop/en/html/inputfiles/parameter_log.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     5.7. [log] section — abICS 2.1-dev documentation
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@@ -33,15 +32,15 @@
           
        
             
   
        
-
        5.7. [log] section
        
+
        5.7. [log] section
        
 
        This section specifies the log file name and the log level.
        
 
        
-
        5.7.1. Input Format
        
+
        5.7.1. Input Format
        
 
        Keywords and their values are specified by a keyword and its value in the form keyword = value.
 Comments can also be entered by adding # (Subsequent characters are ignored).
        
 
        
 
        
-
        5.7.2. Keywords
        
+
        5.7.2. Keywords
        
 
        
 
          
 
        • level
          
@@ -195,7 +194,7 @@ 
          Quick search
          
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/inputfiles/parameter_mlref.html b/docs/develop/en/html/inputfiles/parameter_mlref.html
index 44cac4a4..b0a86669 100644
--- a/docs/develop/en/html/inputfiles/parameter_mlref.html
+++ b/docs/develop/en/html/inputfiles/parameter_mlref.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     5.2. [mlref] section — abICS 2.1-dev documentation
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@@ -34,7 +33,7 @@
           
          
             
   
          
-
          5.2. [mlref] section
          
+
          5.2. [mlref] section
          
 
          Set options for retrieving only atomic configurations from the results of RXMC calculations.
 This is used, for example, to evaluate the accuracy of neural network models and to extend the training data.
 The file format is as follows.
          
@@ -46,12 +45,12 @@ 
          5.2. [mlref] section
-
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          Keywords and their values are specified by a keyword and its value in the form keyword = value.
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          • About replica
            
 
              
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diff --git a/docs/develop/en/html/inputfiles/parameter_observer.html b/docs/develop/en/html/inputfiles/parameter_observer.html
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              This section specifies the physical quantity to be calculated.
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              5.5. [observer] section
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              Keywords and their values are specified by a keyword and its value in the form keyword = value.
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              • [[observer.solver]]
                
 
                This section specifies a physical quantity to be calculated.
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diff --git a/docs/develop/en/html/inputfiles/parameter_sampling.html b/docs/develop/en/html/inputfiles/parameter_sampling.html
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                Specify the parameters of the Monte Carlo (MC) sampling method, such as the number of replicas, the temperature range, and the number of Monte Carlo steps.
 The example is shown as follows.
                
 
                
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                5.1. [sampling] section
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                5.1.1. Input Format
                
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                5.1.1. Input Format
                
 
                Specify a keyword and its value in the form keyword = value.
 Comments can also be entered by adding # (Subsequent characters are ignored).
                
 
                
 
                
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                5.1.2. Keywords
                
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                5.1.2. Keywords
                
 
                  
 
                • About sampling method
                  
 
                  
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diff --git a/docs/develop/en/html/inputfiles/parameter_solver.html b/docs/develop/en/html/inputfiles/parameter_solver.html
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                  5.3. [sampling.solver], [mlref.solver] section
                  
 
                  These sections specify the parameters of solvers, which calculate the energy of a configuration (e.g., atomic positions).
 sampling.solver is used while Monte Carlo sampling, and mlref.solver is used for generating training dataset of a machine learning model.
                  
 
                  In the present version, there are two main types of solvers.
                  
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                  5.3. [sampling.solver], [mlref.solver] s
 
                  
 
        
 
        
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        Keywords and their values are specified by a keyword and its value in the form keyword = value.
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        5.3.2. Keywords
        
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        5.3.2. Keywords
        
 
          
 
        • type
          
 
          Format : str
          
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diff --git a/docs/develop/en/html/inputfiles/parameter_train.html b/docs/develop/en/html/inputfiles/parameter_train.html
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          abics_train creates and trains a regression model from configurations to energies.
 Indeed, abics_train uses an external program to train the model.
 In the current version, only aenet is supported as an external program.
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          • type
            
 
            Format : str
            
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            • 2.1. Prerequisites
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diff --git a/docs/develop/en/html/install/install.html b/docs/develop/en/html/install/install.html
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              abICS requires Python3 (>=3.7).
              
 
              The following Python packages are required.
              
 
                
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                2.1. Prerequisites
 
              
 
              
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              2.2. Install from PyPI
              
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              2.2. Install from PyPI
              
 
              Since abICS is registered in PyPI users can install abICS easily:
              
 
              $ pip3 install abics
 
              
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              2.2. Install from PyPI--prefix=DIRECTORY option (DIRECTORY is the path to the directory where abICS will be installed) .
              
 
              
 
              
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              2.3. Install from source
              
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              2.3. Install from source
              
 
              
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              2.3.1. Download
              
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              2.3.1. Download
              
 
              The source codes of abICS can be obtained from GitHub page .
              
 
              $ git clone https://github.com/issp-center-dev/abICS
              
 
              
 
              
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              2.3.2. Directory structure
              
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              2.3.2. Directory structure
              
 
              The directory structure of abICS is given as follows:
              
 
              .
 |-- COPYING
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              2.3.2. Directory structureabics directory.
              
 
              
 
              
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              • Pass the location of the root directory of abICS as an argument of pip3 install :
                
 
                
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                2.3.3. Install
 
              
 
              
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              • pip3 uninstall abics uninstalls abics from your machine.
                • 
 
              
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diff --git a/docs/develop/en/html/outputfiles/index.html b/docs/develop/en/html/outputfiles/index.html
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              RANK means the rank of process (replica) (0, 1, ...).
              
 
              
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              6.1. RANK/structure.XXX.vasp
              
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              The atomic coordinates for each step are saved in the POSCAR file format of VASP.
 XXX in the filename corresponds to the index of the step.
              
 
              Example:
              
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              6.1. 
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              The lowest-energy structure among the samples in this replica.
              
 
              
 
              
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              The temperature and the total energy for each step in units of eV.
              
 
              Example:
              
 
              0      0.1034076       -41690.28269769395
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              The total energy for each step in units of eV in the Numpy binary format.
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              Example:
              
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              The temperature for each step in units of eV in the Numpy binary format.
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              Example:
              
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              6.5. 
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              6.6. RANK/Trank_hist.npy
              
 
              (ONLY for RXMC)
 The rank (index) of the temperature for each step in the Numpy binary format.
 Users can load it as darray by using numpy.load('Trank_hist.npy').
              
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              (ONLY for PAMC)
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              Example:
              
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              Acceptance ratio of Monte Carlo steps for each temperature.
 The first column is temperature and the second column is acceptance ratio (number of accepted / number of trials).
              
 
              
 
              
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              The logarithm of the partition function, \(\log Z_i/Z_0\) where \(i\) is the index of temperature.
              
 
                
 
              • The 1st column is temperature \(T_i\).
                • 
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                6.9. 
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                Canonical expectation value \(\langle O \rangle\) and statistical error \(\sigma[O]\) of an observable \(O\) for each temperature.
 <name> is the name of the observable which is specified by name keyword in [[observer.solver]] section of the input file.
                
 
                  
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-Search.setIndex({"docnames": ["about/index", "about/info", "acknowledge/index", "algorithm/index", "contact/index", "how_to_use/index", "index", "inputfiles/index", "inputfiles/parameter_config", "inputfiles/parameter_log", "inputfiles/parameter_mlref", "inputfiles/parameter_observer", "inputfiles/parameter_sampling", "inputfiles/parameter_solver", "inputfiles/parameter_train", "install/index", "install/install", "outputfiles/index", "tools/index", "tools/tools_abicsRXsepT", "tools/tools_st2abics", "tutorial/aenet", "tutorial/index", "tutorial/qe", "tutorial/vasp"], "filenames": ["about/index.rst", "about/info.rst", "acknowledge/index.rst", "algorithm/index.rst", "contact/index.rst", "how_to_use/index.rst", "index.rst", "inputfiles/index.rst", "inputfiles/parameter_config.rst", "inputfiles/parameter_log.rst", "inputfiles/parameter_mlref.rst", "inputfiles/parameter_observer.rst", "inputfiles/parameter_sampling.rst", "inputfiles/parameter_solver.rst", "inputfiles/parameter_train.rst", "install/index.rst", "install/install.rst", "outputfiles/index.rst", "tools/index.rst", "tools/tools_abicsRXsepT.rst", "tools/tools_st2abics.rst", "tutorial/aenet.rst", "tutorial/index.rst", "tutorial/qe.rst", "tutorial/vasp.rst"], "titles": ["1. 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\ No newline at end of file
+Search.setIndex({"docnames": ["about/index", "about/info", "acknowledge/index", "algorithm/index", "contact/index", "how_to_use/index", "index", "inputfiles/index", "inputfiles/parameter_config", "inputfiles/parameter_log", "inputfiles/parameter_mlref", "inputfiles/parameter_observer", "inputfiles/parameter_sampling", "inputfiles/parameter_solver", "inputfiles/parameter_train", "install/index", "install/install", "outputfiles/index", "tools/index", "tools/tools_abicsRXsepT", "tools/tools_st2abics", "tutorial/aenet", "tutorial/index", "tutorial/qe", "tutorial/vasp"], "filenames": ["about/index.rst", "about/info.rst", "acknowledge/index.rst", "algorithm/index.rst", "contact/index.rst", "how_to_use/index.rst", "index.rst", "inputfiles/index.rst", "inputfiles/parameter_config.rst", "inputfiles/parameter_log.rst", "inputfiles/parameter_mlref.rst", "inputfiles/parameter_observer.rst", "inputfiles/parameter_sampling.rst", "inputfiles/parameter_solver.rst", "inputfiles/parameter_train.rst", "install/index.rst", "install/install.rst", "outputfiles/index.rst", "tools/index.rst", "tools/tools_abicsRXsepT.rst", "tools/tools_st2abics.rst", "tutorial/aenet.rst", "tutorial/index.rst", "tutorial/qe.rst", "tutorial/vasp.rst"], "titles": ["1. About abICS", "1.1. What is abICS ?", "9. Acknowledgement", "8. Algorithm", "10. Contacts", "3. Basic Usage", "Welcome to abICS\u2019s documentation!", "5. Input Files Format", "5.6. [config] section", "5.7. [log] section", "5.2. [mlref] section", "5.5. [observer] section", "5.1. [sampling] section", "5.3. [sampling.solver], [mlref.solver] section", "5.4. [train] section", "2. Install", "2.1. Prerequisites", "6. Output Files Format", "7. Miscellaneous tools", "7.2. abicsRXsepT", "7.1. st2abics", "4.1. Constructing a neural network model", "4. 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"st2abic": 20, "construct": 21, "gnu": 21, "parallel": 21, "gener": 21, "toml": 21, "ii": 21, "iii": 21, "qe": [21, 23], "predict": 21, "run": 21, "energi": 21, "annet": 21, "via": 21, "lammp": 21, "interfac": 21, "aenetpylammp": 21, "tutori": 22, "exampl": [23, 24], "us": [23, 24], "quantumespresso": 23, "execut": [23, 24], "analysi": [23, 24]}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 60}, "alltitles": {"About abICS": [[0, "about-abics"]], "What is abICS ?": [[1, "what-is-abics"]], "Developers": [[1, "developers"]], "Version information": [[1, "version-information"]], "License": [[1, "license"]], "Copyright": [[1, "copyright"]], "Acknowledgement": [[2, "acknowledgement"]], "Algorithm": [[3, "algorithm"]], "Replica exchange Monte Carlo method": [[3, "replica-exchange-monte-carlo-method"]], "Population Annealing Monte Carlo": [[3, "population-annealing-monte-carlo"]], "About configuration and update": [[3, "about-configuration-and-update"]], "Contacts": [[4, "contacts"]], "Basic Usage": [[5, "basic-usage"]], "Active learning": [[5, "active-learning"]], "Preparing an abICS control file": [[5, "preparing-an-abics-control-file"]], "Preparing a reference file for first-principles solvers": [[5, "preparing-a-reference-file-for-first-principles-solvers"]], "Specific notes for first-principles solvers": [[5, "specific-notes-for-first-principles-solvers"]], "VASP": [[5, "vasp"]], "Quantum Espresso": [[5, "quantum-espresso"]], "OpenMX": [[5, "openmx"]], "Preparing a reference file for training and evaluating the machine learning model": [[5, "preparing-a-reference-file-for-training-and-evaluating-the-machine-learning-model"]], "Machine learning trainer/calculator-specific notes": [[5, "machine-learning-trainer-calculator-specific-notes"]], "aenet": [[5, "aenet"]], "Creating a set of training data": [[5, "creating-a-set-of-training-data"]], "Creating a neural network": [[5, "creating-a-neural-network"]], "Monte Carlo sampling": [[5, "monte-carlo-sampling"], [21, "monte-carlo-sampling"]], "Welcome to abICS\u2019s documentation!": [[6, "welcome-to-abics-s-documentation"]], "Contents:": [[6, null]], "Indices and tables": [[6, "indices-and-tables"]], "Input Files Format": [[7, "input-files-format"]], "[config] section": [[8, "config-section"]], "Input Format": [[8, "input-format"], [9, "input-format"], [10, "input-format"], [11, "input-format"], [12, "input-format"], [13, "input-format"], [14, "input-format"], [20, "input-format"]], "Key words": [[8, "key-words"], [10, "key-words"], [11, "key-words"], [14, "key-words"]], "In the case of solver.type != \"potts\"": [[8, "in-the-case-of-solver-type-potts"]], "In the case of solver.type = \"potts\"": [[8, "id2"]], "[log] section": [[9, "log-section"]], "Keywords": [[9, "keywords"], [12, "keywords"], [13, "keywords"], [20, "keywords"]], "[mlref] section": [[10, "mlref-section"]], "[observer] section": [[11, "observer-section"]], "[sampling] section": [[12, "sampling-section"]], "[sampling.solver], [mlref.solver] section": [[13, "sampling-solver-mlref-solver-section"]], "[train] section": [[14, "train-section"]], "Install": [[15, "install"], [16, "install"]], "Prerequisites": [[16, "prerequisites"]], "Install from PyPI": [[16, "install-from-pypi"]], "Install from source": [[16, "install-from-source"]], "Download": [[16, "download"]], "Directory structure": [[16, "directory-structure"]], "Uninstall": [[16, "uninstall"]], "Output Files Format": [[17, "output-files-format"]], "RANK/structure.XXX.vasp": [[17, "rank-structure-xxx-vasp"]], "RANK/minE.vasp": [[17, "rank-mine-vasp"]], "RANK/obs.dat": [[17, "rank-obs-dat"]], "RANK/obs_save.npy": [[17, "rank-obs-save-npy"]], "RANK/kT_hist.npy": [[17, "rank-kt-hist-npy"]], "RANK/Trank_hist.npy": [[17, "rank-trank-hist-npy"]], "RANK/logweight_hist.npy": [[17, "rank-logweight-hist-npy"]], "RANK/acceptance_ratio.dat": [[17, "rank-acceptance-ratio-dat"]], "logZ.dat": [[17, "logz-dat"]], ".dat": [[17, "name-dat"]], "Miscellaneous tools": [[18, "miscellaneous-tools"]], "abicsRXsepT": [[19, "abicsrxsept"]], "st2abics": [[20, "st2abics"]], "Constructing a neural network model": [[21, "constructing-a-neural-network-model"]], "Preparation": [[21, "preparation"]], "Installation of aenet": [[21, "installation-of-aenet"]], "Installation of GNU parallel": [[21, "installation-of-gnu-parallel"]], "Preparation of input files for training data set generation": [[21, "preparation-of-input-files-for-training-data-set-generation"]], "Preparation of the abICS control file (input.toml)": [[21, "preparation-of-the-abics-control-file-input-toml"], [21, "id1"], [21, "id2"]], "(i) [mlref] section": [[21, "i-mlref-section"]], "(ii) [mlref.solver] section": [[21, "ii-mlref-solver-section"]], "(iii) [config] section": [[21, "iii-config-section"]], "Preparation of the QE reference file": [[21, "preparation-of-the-qe-reference-file"]], "Preparation of input files for training the neural network": [[21, "preparation-of-input-files-for-training-the-neural-network"]], "(i) [train] section": [[21, "i-train-section"]], "Preparation of input files for aenet": [[21, "preparation-of-input-files-for-aenet"]], "generate": [[21, "generate"]], "train": [[21, "train"]], "predict": [[21, "predict"]], "Running the calculation": [[21, "running-the-calculation"], [21, "id3"]], "Preparation of input files": [[21, "preparation-of-input-files"]], "(i) [sampling] section": [[21, "i-sampling-section"]], "(ii) [sampling.solver] section": [[21, "ii-sampling-solver-section"]], "Predict energy of annet model via LAMMPS interface": [[21, "predict-energy-of-annet-model-via-lammps-interface"]], "Install aenetPyLammps": [[21, "install-aenetpylammps"]], "Training": [[21, "training"]], "Sampling": [[21, "sampling"]], "Input file for prediction": [[21, "input-file-for-prediction"]], "Input for Sampling": [[21, "input-for-sampling"]], "Tutorial": [[22, "tutorial"]], "Example by using QuantumESPRESSO": [[23, "example-by-using-quantumespresso"]], "Preparing the input files for abICS": [[23, "preparing-the-input-files-for-abics"], [24, "preparing-the-input-files-for-abics"]], "Preparing the input file of QE": [[23, "preparing-the-input-file-of-qe"]], "Execution and analysis": [[23, "execution-and-analysis"], [24, "execution-and-analysis"]], "Example by using VASP": [[24, "example-by-using-vasp"]], "Preparing the input file of VASP": [[24, "preparing-the-input-file-of-vasp"]]}, "indexentries": {}})
\ No newline at end of file
diff --git a/docs/develop/en/html/tools/index.html b/docs/develop/en/html/tools/index.html
index ad007842..755cdb09 100644
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+++ b/docs/develop/en/html/tools/index.html
@@ -1,17 +1,16 @@
-
 
 
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     7. Miscellaneous tools — abICS 2.1-dev documentation
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              7. Miscellaneous tools
              
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              7. Miscellaneous tools
              
 
              abICS comes with a few tools for facilitating typical workflows.
              
 
                
 
              • st2abics for preparing an abICS input file from a structure file.
                • 
@@ -118,7 +117,7 @@ 
                Quick search
                
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/en/html/tools/tools_abicsRXsepT.html b/docs/develop/en/html/tools/tools_abicsRXsepT.html
index 0bf639c9..a93e1a23 100644
--- a/docs/develop/en/html/tools/tools_abicsRXsepT.html
+++ b/docs/develop/en/html/tools/tools_abicsRXsepT.html
@@ -1,17 +1,16 @@
-
 
 
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     7.2. abicsRXsepT — abICS 2.1-dev documentation
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                7.2. abicsRXsepT
                
+
                7.2. abicsRXsepT
                
 
                This tool is for reordering the resulting structures and energies at each sampling step of
 a RXMC run by temperature. It is used after an abICS RXMC run is finished as:
                
 
                $ mpiexec -np NPROCS abicsRXsepT input.toml NSKIP
@@ -117,7 +116,7 @@ 
                Quick search
                
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/en/html/tools/tools_st2abics.html b/docs/develop/en/html/tools/tools_st2abics.html
index 1efef758..73fdf506 100644
--- a/docs/develop/en/html/tools/tools_st2abics.html
+++ b/docs/develop/en/html/tools/tools_st2abics.html
@@ -1,17 +1,16 @@
-
 
 
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     7.1. st2abics — abICS 2.1-dev documentation
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                7.1. st2abics
                
+
                7.1. st2abics
                
 
                It is sometimes quite tedious to prepare the [config] section in abICS input files.
 To facilitate this, we provide the st2abics tool, which takes a structure file readable by pymatgen
 and converts it to an abICS input template with the [config] section filled in. An additional control file is required to
@@ -64,13 +63,13 @@ 
                7.1. st2abicsThe resulting files (abics_MgAl2O4.toml, abics_CuZn.toml, and abics_BZY.toml in the above example) can be used as abICS input after
 filling in the [mlref], [train], [sampling] and [observer] sections.
                
 
                
-
                7.1.1. Input Format
                
+
                7.1.1. Input Format
                
 
                Examples of st2abics input files can be found in examples/st2abics
 (st2abics_CuZn.toml, st2abics_MgAl2O4.toml, and st2abics_BZY.toml in the above example).
                
 
                The format is similar to [config] section of abICS input file.
                
 
                
 
                
-
                7.1.2. Keywords
                
+
                7.1.2. Keywords
                
 
                  
 
                • supercell
                  
 
                  Format : list
                  
@@ -210,7 +209,7 @@ 
                  Quick search
                  
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/en/html/tutorial/aenet.html b/docs/develop/en/html/tutorial/aenet.html
index 93dcf344..0dd183aa 100644
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     4.1. Constructing a neural network model — abICS 2.1-dev documentation
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                  4.1. Constructing a neural network model
                  
+
                  4.1. Constructing a neural network model
                  
 
                  This section contains instructions on how to construct a neural network using aenet
 to reproduce first-principles energies from Quantum ESPRESSO (QE).
 Here, we will consider the temperature-dependent degree of Mg/Al inversion in
@@ -44,9 +43,9 @@
 In the following, we briefly describe the installation of aenet and GNU parallel, but you may skip the section if they are preinstalled in your system.
 We will also use ohtaka, the supercomputer system B of the Institute for Solid State Physics, as the environment for running the calculations.
                  
 
                  
-
                  4.1.1. Preparation
                  
+
                  4.1.1. Preparation
                  
 
                  
-
                  Installation of aenet
                  
+
                  Installation of aenet
                  
 
                  In abICS, we use aenet to build neural network models.
 You can download aenet from http://ann.atomistic.net.
 Follow the Installation instructions in the Documentation to install it.
@@ -55,7 +54,7 @@ 
                  Installation of aenet
 
                  
 
                  
-
                  Installation of GNU parallel
                  
+
                  Installation of GNU parallel
                  
 
                  In this tutorial, we will use GNU parallel to run first-principles calculations with Quantum Espresso in parallel.
 Therefore, you need to install GNU parallel first.
 GNU parallel can be downloaded from https://www.gnu.org/software/parallel/ (on a Mac, it can also be installed directly by homebrew).
@@ -68,12 +67,12 @@ 
                  Installation of GNU parallel
-
                  4.1.2. Preparation of input files for training data set generation
                  
+
                  4.1.2. Preparation of input files for training data set generation
                  
 
                  A set of training data is required for creating a neural network
 that relate the configurations of atoms as input and the energy as output by the first-principle calculations.
 To generate the data set, the input files need to be prepared for both abICS and the first-principle solver.
                  
 
                  
-
                  Preparation of the abICS control file (input.toml)
                  
+
                  Preparation of the abICS control file (input.toml)
                  
 
                  This file contains the definition of the lattice structure to be calculated, the control of the entire active learning cycles by abICS, and the parameters for the replica exchange Monte Carlo method.
 By using the st2abics tool, you can automatically generate the input.toml template from the crystal structure file.
                  
 
                  $ cd [example_dir].
@@ -82,7 +81,7 @@ 
                  Preparation of the abICS control file (input.toml in more detail.
                  
 
                  
-
                  (i) [mlref] section
                  
+
                  (i) [mlref] section
                  
 
                  [mlref]
 nreplicas = 8
 ndata = 5
@@ -94,7 +93,7 @@ 
                  (i) [mlref]nsteps/sample_frequency in [sampling] section.
                  
 
                  
 
                  
-
                  (ii) [mlref.solver] section
                  
+
                  (ii) [mlref.solver] section
                  
 
                  [mlref.solver] # Set up a reference ab initio solver.
 type = 'qe'
 base_input_dir = ['./baseinput_ref', './baseinput_ref', './baseinput_ref'] #, './baseinput_ref']
@@ -116,7 +115,7 @@ 
                  (ii) [mlref.sol
 When a model is employed for the data generation in which some atomic species are ignored, they are specified in ignore-species.
                  
 
                  
 
                  
-
                  (iii) [config] section
                  
+
                  (iii) [config] section
                  
 
                  [config] # Set up information about the crystal lattice and the atoms and vacancies on the lattice.
 unitcell = [[8.1135997772, 0.0000000000000000, 0.0000000000000000],
             [0.0000000000000000, 8.1135997772, 0.0000000000000000],
@@ -139,7 +138,7 @@ 
                  (iii) [config]<
 based on this information, and the input files for the first-principle calculation are produced.
 Once abics_sampling is executed, the input files will be generated from the atomic positions obtained from the Monte Carlo sampling.
                  
 
                  
-
                  Preparation of the QE reference file
                  
+
                  Preparation of the QE reference file
                  
 
                  Place the input file to be referenced in the QE scf calculation in baseinput_ref.
 The following is a description of the scf.in file in the sample directory.
                  
 
                  &CONTROL
@@ -186,13 +185,13 @@ 
                  Preparation of the QE reference file
-
                  4.1.3. Preparation of input files for training the neural network
                  
+
                  4.1.3. Preparation of input files for training the neural network
                  
 
                  In this tutorial we use aenet to train the neural netowrk. We need to prepare the input files for
 abICS and aenet.
                  
 
                  
-
                  Preparation of the abICS control file (input.toml)
                  
+
                  Preparation of the abICS control file (input.toml)
                  
 
                  
-
                  (i) [train] section
                  
+
                  (i) [train] section
                  
 
                  [train] # Configure the model trainer.
 type = 'aenet'
 base_input_dir = '. /aenet_train_input'
@@ -211,11 +210,11 @@ 
                  (i) [train]
 
                  
 
                  
-
                  Preparation of input files for aenet
                  
+
                  Preparation of input files for aenet
                  
 
                  Place the input files for aenet in the generate, train, and predict directories
 in the directory set in the base_input_dir of the [train] section.
                  
 
                  
-
                  generate
                  
+
                  generate
                  
 
                  aenet compiles the atomic configuration and energy data for training into an intermediate binary format
 that is converted into atomic environment descriptor-energy relationships before training.
 Input files for generate.x that perform this conversion are placed in the generate directory.
                  
@@ -263,7 +262,7 @@ 
                  generategenerate.in, and run generate.x.
                  
 
                  
 
                  
-
                  train
                  
+
                  train
                  
 
                  Place the input file for train.x,
 which reads the training data generated by generate and trains,
 in the train directory.
@@ -293,7 +292,7 @@ 
                  train
 the neural network structure, and the activation function.
                  
 
                  
 
                  
-
                  predict
                  
+
                  predict
                  
 
                  Place the input file predict.in for predict.x in the predict directory
 to evaluate the energy for the input coordinates using the trained potential model.
                  
 
                  TYPES
@@ -315,7 +314,7 @@ 
                  predict
-
                  Running the calculation
                  
+
                  Running the calculation
                  
 
                  Now the input files have been prepared, we proceed to describe how to run the calculation.
 A sample script AL.sh is prepared to simplify the calculation procedure.
 run_pw.sh is used to run QE calculations; it is called inside parallel_run.sh, which will be described later.
@@ -385,16 +384,16 @@ 
                  Running the calculation
 
                  
 
                  
-
                  4.2. Monte Carlo sampling
                  
+
                  4.2. Monte Carlo sampling
                  
 
                  Next, we use the trained neural network potential for Monte Carlo samplings by abICS.
                  
 
                  
-
                  4.2.1. Preparation of input files
                  
+
                  4.2.1. Preparation of input files
                  
 
                  Several parameters need to be set in the abICS control file to perform the sampling as follows.
                  
 
                  
-
                  Preparation of the abICS control file (input.toml)
                  
+
                  Preparation of the abICS control file (input.toml)
                  
 
                  The calculation parameters are specified in [sampling] section concerning the Replica Exchange Monte carlo method.
                  
 
                  
-
                  (i) [sampling] section
                  
+
                  (i) [sampling] section
                  
 
                  [sampling]
 nreplicas = 8
 nprocs_per_replica = 1
@@ -411,7 +410,7 @@ 
                  (i) [sampling]<
 This time, we will use anet’s predict.x as the energy solver for RXMC calculations. Currently, the mpi version of predict.x is not supported, so nprocs_per_replica should be 1.
                  
 
                  
 
                  
-
                  (ii) [sampling.solver] section
                  
+
                  (ii) [sampling.solver] section
                  
 
                  [sampling.solver] # Configure the solver used for RXMC calculations
 type = 'aenet'
 path= 'predict.x-2.0.4-ifort_serial'
@@ -433,7 +432,7 @@ 
                  (ii) [sampling.
 
                  
 
                  
 
                  
-
                  4.2.2. Running the calculation
                  
+
                  4.2.2. Running the calculation
                  
 
                  The sample script MC.sh is provided to simplify the calculation procedure. The content of the script is as follows.
                  
 
                  #! /bin/sh
 #SBATCH -p i8cpu
@@ -478,12 +477,12 @@ 
                  4.2.2. Running the calculation
-
                  4.2.3. Predict energy of annet model via LAMMPS interface
                  
+
                  4.2.3. Predict energy of annet model via LAMMPS interface
                  
 
                  abICS can call the aenet library via the LAMMPS interface (aenetPyLammps).
 This is faster than calling aenet directly because it does not need file I/O.
 The set of input files used in this tutorial can be found in examples/active_learning_qe.
                  
 
                  
-
                  Install aenetPyLammps
                  
+
                  Install aenetPyLammps
                  
 
                  To use aenetPyLammps, you need to install aenet-lammps and lammps.
                  
 
                  
 
                  
-
                  Training
                  
+
                  Training
                  
 
                  The training procedure is the same as the previous section.
                  
 
                  
 
                  
-
                  Sampling
                  
+
                  Sampling
                  
 
                  
-
                  Input file for prediction
                  
+
                  Input file for prediction
                  
 
                  Instead of the input file predict.in for predict.x,
 place the input file in.lammps under the predict:
                  
 
                  pair_style      aenet
@@ -532,7 +531,7 @@ 
                  Input file for predictionin.lammmps is written in the README of aenet-lammps repository.
                  
 
                  
 
                  
-
                  Input for Sampling
                  
+
                  Input for Sampling
                  
 
                  Change the type and run_scheme in the [sampling.solver] section of the input file to 'aenetPyLammps' and 'function', respectively.
                  
 
                  [sampling.solver]
 type = 'aenetPyLammps'
@@ -618,7 +617,7 @@ 
                  Quick search
                  
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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       & Alabaster 0.7.13
       
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diff --git a/docs/develop/en/html/tutorial/index.html b/docs/develop/en/html/tutorial/index.html
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     4. Tutorial — abICS 2.1-dev documentation
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                  4. Tutorial
                  
+
                  4. Tutorial
                  
 
                  In this tutorial, we demonstrate the calculation of the degree of inversion of Mg and Al atoms
 in an ionic crystal \({\rm Mg}{\rm Al}_2 {\rm O}_4\).
 Input files are provided in examples/active_learning_qe/ .
                  
@@ -126,7 +125,7 @@ 
                  Quick search
                  
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/tutorial/qe.html b/docs/develop/en/html/tutorial/qe.html
index 747b8331..9316a1e0 100644
--- a/docs/develop/en/html/tutorial/qe.html
+++ b/docs/develop/en/html/tutorial/qe.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     Example by using QuantumESPRESSO — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
    
@@ -31,9 +30,9 @@
           
                  
             
   
                  
-
                  Example by using QuantumESPRESSO
                  
+
                  Example by using QuantumESPRESSO
                  
 
                  
-
                  Preparing the input files for abICS
                  
+
                  Preparing the input files for abICS
                  
 
                  The input file of abICS is input_qe.toml .
                  
 
                  [sampling]
 nreplicas = 2
@@ -160,7 +159,7 @@ 
                  Preparing the input files for abICSAl and 8 Mg atoms on the lattice specified by [[config.defect_structure]].
                  
 
                  
 
                  
-
                  Preparing the input file of QE
                  
+
                  Preparing the input file of QE
                  
 
                  abICS generates the input files of the solver from the internally-held structure information, but information other than the structure such as pseudopotential information must be supplied by the user.
 In the case of QE, such information is specified by scf.in in the directory specified by base_input_dir in the format of the input file of pw.x.
 Based on this file, an input file with unit cells and atomic structure is automatically generated.
                  
@@ -175,7 +174,7 @@ 
                  Preparing the input file of QE
-
                  Execution and analysis
                  
+
                  Execution and analysis
                  
 
                  Please refer to Basic Usage section for information on setting the number of processes and options for running MPI.
                  
 
                  mpiexec -np 2 abics_sampling input_qe.toml
 
                  
@@ -268,7 +267,7 @@ 
                  Quick search
                  
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/en/html/tutorial/vasp.html b/docs/develop/en/html/tutorial/vasp.html
index 73134e6b..9883df4d 100644
--- a/docs/develop/en/html/tutorial/vasp.html
+++ b/docs/develop/en/html/tutorial/vasp.html
@@ -1,17 +1,16 @@
-
 
 
-
+
   
     
     
 
     Example by using VASP — abICS 2.1-dev documentation
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
     
     
    
@@ -31,9 +30,9 @@
           
                  
             
   
                  
-
                  Example by using VASP
                  
+
                  Example by using VASP
                  
 
                  
-
                  Preparing the input files for abICS
                  
+
                  Preparing the input files for abICS
                  
 
                  The input file of abICS is input_vasp.toml .
 Below, input_vasp.toml in examples/spinel is explained as an example.
 Only the [sampling.solver] section is differnt from that of QuantumESPRESSO.
@@ -53,7 +52,7 @@ 
                  Preparing the input files for abICSvasp with MPI_Comm_spawn, so give mpi_spawn_ready as run_scheme .To use VASP as a solver, a patch must be applied to use MPI_COMM_SPAWN. If you wish to use it, please contact us (the e-mail address is written in Contacts .
                  
 
                  
 
                  
-
                  Preparing the input file of VASP
                  
+
                  Preparing the input file of VASP
                  
 
                  abICS generates the input files of the solver from the internal atomic structure, but information other than the structure, such as pseudopotential information, must be supplied by the user.
 In the case of VASP, such information is specified by INCAR, POSCAR,  KPOINTS and POTCAR in  base_input_dir. Here, POTCAR file is not contained in the base_input_dir due to the VASP license. Before the calculation, generate  POTCAR file from the O, Al, Mg pesudo potential files.
 Based on these files, an input file with unit cells and atomic structure is automatically generated.
                  
@@ -67,7 +66,7 @@ 
                  Preparing the input file of VASP
-
                  Execution and analysis
                  
+
                  Execution and analysis
                  
 
                  The procedures of execution and analysis are same as those of QE.
 If you do with 17 replicas and 1000 steps same as the exapmle of QE, the following result will be obtained
                  
 ../_images/doi_vasp.png
@@ -139,7 +138,7 @@ 
                  Quick search
                  
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/ja/html/_sources/about/info.rst.txt b/docs/develop/ja/html/_sources/about/info.rst.txt
index d5d3f8e3..c94502c3 100644
--- a/docs/develop/ja/html/_sources/about/info.rst.txt
+++ b/docs/develop/ja/html/_sources/about/info.rst.txt
@@ -51,6 +51,21 @@ abICSは以下のメンバーで開発しています.
 --------------
 本ソフトウェアのプログラムパッケージおよびソースコード一式はGNU General Public License version 3 (GPL v3) に準じて配布されています。
 
+abICSを引用する際は, 以下の文献を引用してください。
+
+Shusuke Kasamatsu, Yuichi Motoyama, Kazuyoshi Yoshimi, Tatsumi Aoyama, “Configuration sampling in multi-component multi-sublattice systems enabled by ab Initio Configuration Sampling Toolkit (abICS)”, `arXiv:2309.04769 `_.
+
+Bibtex:
+
+@misc{kasamatsu2023configuration,
+title={Configuration sampling in multi-component multi-sublattice systems enabled by ab Initio Configuration Sampling Toolkit (abICS)},
+author={Shusuke Kasamatsu and Yuichi Motoyama and Kazuyoshi Yoshimi and Tatsumi Aoyama},
+year={2023},
+eprint={2309.04769},
+archivePrefix={arXiv},
+primaryClass={cond-mat.mtrl-sci}
+}
+
 コピーライト
 ------------------
 
diff --git a/docs/develop/ja/html/_static/basic.css b/docs/develop/ja/html/_static/basic.css
index 7577acb1..30fee9d0 100644
--- a/docs/develop/ja/html/_static/basic.css
+++ b/docs/develop/ja/html/_static/basic.css
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {
diff --git a/docs/develop/ja/html/_static/documentation_options.js b/docs/develop/ja/html/_static/documentation_options.js
index 749db245..678f874f 100644
--- a/docs/develop/ja/html/_static/documentation_options.js
+++ b/docs/develop/ja/html/_static/documentation_options.js
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '2.1-dev',
     LANGUAGE: 'ja',
     COLLAPSE_INDEX: false,
diff --git a/docs/develop/ja/html/_static/pygments.css b/docs/develop/ja/html/_static/pygments.css
index 691aeb82..0d49244e 100644
--- a/docs/develop/ja/html/_static/pygments.css
+++ b/docs/develop/ja/html/_static/pygments.css
@@ -17,6 +17,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
 .highlight .gr { color: #FF0000 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */
diff --git a/docs/develop/ja/html/_static/searchtools.js b/docs/develop/ja/html/_static/searchtools.js
index 97d56a74..7918c3fa 100644
--- a/docs/develop/ja/html/_static/searchtools.js
+++ b/docs/develop/ja/html/_static/searchtools.js
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**
diff --git a/docs/develop/ja/html/_static/sphinx_highlight.js b/docs/develop/ja/html/_static/sphinx_highlight.js
index aae669d7..8a96c69a 100644
--- a/docs/develop/ja/html/_static/sphinx_highlight.js
+++ b/docs/develop/ja/html/_static/sphinx_highlight.js
@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});
diff --git a/docs/develop/ja/html/_static/translations.js b/docs/develop/ja/html/_static/translations.js
index 282c78a7..817b128c 100644
--- a/docs/develop/ja/html/_static/translations.js
+++ b/docs/develop/ja/html/_static/translations.js
@@ -2,8 +2,7 @@ Documentation.addTranslations({
     "locale": "ja",
     "messages": {
         "%(filename)s — %(docstitle)s": "%(filename)s — %(docstitle)s",
-        "© Copyright %(copyright)s.": "© Copyright %(copyright)s.",
-        "© Copyright %(copyright)s.": "© Copyright %(copyright)s.",
+        "© %(copyright_prefix)s %(copyright)s.": "",
         ", in ": ", in ",
         "About these documents": "\u3053\u306e\u30c9\u30ad\u30e5\u30e1\u30f3\u30c8\u306b\u3064\u3044\u3066",
         "Automatically generated list of changes in version %(version)s": "\u30d0\u30fc\u30b8\u30e7\u30f3 %(version)s \u306e\u5909\u66f4\u70b9\uff08\u3053\u306e\u30ea\u30b9\u30c8\u306f\u81ea\u52d5\u751f\u6210\u3055\u308c\u3066\u3044\u307e\u3059\uff09",
diff --git a/docs/develop/ja/html/about/index.html b/docs/develop/ja/html/about/index.html
index 5b6cfb4f..18b1e501 100644
--- a/docs/develop/ja/html/about/index.html
+++ b/docs/develop/ja/html/about/index.html
@@ -1,18 +1,17 @@
-
 
 
-
+
   
     
     
 
     1. abICS とは？ — abICS 2.1-dev ドキュメント
-    
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
+    
     
     
     
@@ -34,7 +33,7 @@
           
                  
             
   
                  
-
                  1. abICS とは？
                  
+
                  1. abICS とは？
                  
 
                  
 
                    
 
                  • 1.1. 概要
                    • 
@@ -118,7 +117,7 @@ 
                    クイック検索
                    
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/ja/html/about/info.html b/docs/develop/ja/html/about/info.html
index c7fe9d8e..54a67024 100644
--- a/docs/develop/ja/html/about/info.html
+++ b/docs/develop/ja/html/about/info.html
@@ -1,18 +1,17 @@
-
 
 
-
+
   
     
     
 
     1.1. 概要 — abICS 2.1-dev ドキュメント
-    
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
+    
     
     
     
@@ -34,7 +33,7 @@
           
                    
             
   
                    
-
                    1.1. 概要
                    
+
                    1.1. 概要
                    
 
                    abICSは、第一原理計算を再現する機械学習モデルを訓練し、
 不規則系での統計熱力学サンプリングを高速に
 実行するためのソフトウェアフレームワークです。
@@ -46,7 +45,7 @@ 
                    1.1. 概要
-
                    1.2. 開発者
                    
+
                    1.2. 開発者
                    
 
                    abICSは以下のメンバーで開発しています.
                    
 
                      
 
                    • 
@@ -75,7 +74,7 @@ 
                      1.2. 開発者
 
                    
 
                    
-
                    1.3. バージョン履歴
                    
+
                    1.3. バージョン履歴
                    
 
                      
 
                    • ver.2.1.0    : 2023/06/12.
                      • 
 
                    • ver.2.0.1    : 2022/11/04.
                      • 
@@ -86,11 +85,22 @@ 
                      1.3. バージョン履歴
-
                      1.4. ライセンス
                      
+
                      1.4. ライセンス
                      
 
                      本ソフトウェアのプログラムパッケージおよびソースコード一式はGNU General Public License version 3 (GPL v3) に準じて配布されています。
                      
+
                      abICSを引用する際は, 以下の文献を引用してください。
                      
+
                      Shusuke Kasamatsu, Yuichi Motoyama, Kazuyoshi Yoshimi, Tatsumi Aoyama, “Configuration sampling in multi-component multi-sublattice systems enabled by ab Initio Configuration Sampling Toolkit (abICS)”, arXiv:2309.04769.
                      
+
                      Bibtex:
                      
+
                      @misc{kasamatsu2023configuration,
+title={Configuration sampling in multi-component multi-sublattice systems enabled by ab Initio Configuration Sampling Toolkit (abICS)},
+author={Shusuke Kasamatsu and Yuichi Motoyama and Kazuyoshi Yoshimi and Tatsumi Aoyama},
+year={2023},
+eprint={2309.04769},
+archivePrefix={arXiv},
+primaryClass={cond-mat.mtrl-sci}
+}
                      
 
                    
 
                    
-
                    1.5. コピーライト
                    
+
                    1.5. コピーライト
                    
 
                    (c) 2019- The University of Tokyo. All rights reserved.
                    
 
                    本ソフトウェアは2019, 2022年度 東京大学物性研究所 ソフトウェア高度化プロジェクトの支援を受け開発されており、その著作権は東京大学が所持しています。
                    
 
                    
@@ -169,7 +179,7 @@ 
                    クイック検索
                    
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/ja/html/acknowledge/index.html b/docs/develop/ja/html/acknowledge/index.html
index efe7ba0d..ccddd9c4 100644
--- a/docs/develop/ja/html/acknowledge/index.html
+++ b/docs/develop/ja/html/acknowledge/index.html
@@ -1,18 +1,17 @@
-
 
 
-
+
   
     
     
 
     9. 謝辞 — abICS 2.1-dev ドキュメント
-    
-    
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+    
+    
+    
+    
+    
+    
     
     
     
@@ -34,7 +33,7 @@
           
                    
             
   
                    
-
                    9. 謝辞
                    
+
                    9. 謝辞
                    
 
                    このソフトウェアの開発は, 様々なプロジェクトとコンピューター資源の提供によりサポートされてきました。この場を借りて感謝します。
                    
 
                      
 
                    • ポスト「京」重点課題5
                      • 
@@ -112,7 +111,7 @@ 
                      クイック検索
                      
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/ja/html/algorithm/index.html b/docs/develop/ja/html/algorithm/index.html
index 6295251f..fafb5128 100644
--- a/docs/develop/ja/html/algorithm/index.html
+++ b/docs/develop/ja/html/algorithm/index.html
@@ -1,18 +1,17 @@
-
 
 
-
+
   
     
     
 
     8. アルゴリズム — abICS 2.1-dev ドキュメント
-    
-    
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+    
+    
+    
+    
+    
+    
     
     
     
@@ -35,7 +34,7 @@
           
                      
             
   
                      
-
                      8. アルゴリズム
                      
+
                      8. アルゴリズム
                      
 
                      abICSは、拡張アンサンブル法と任意のエネルギー計算ソフトウェアを組み合わせるために設計されています。現在は、
 レプリカ交換モンテカルロ法およびポピュレーションアニーリングモンテカルロ法が実装されています。
                      
 
                        
@@ -47,7 +46,7 @@ 
                        8. アルゴリズム
-
                        8.1. レプリカ交換モンテカルロ法
                        
+
                        8.1. レプリカ交換モンテカルロ法
                        
 
                        広く使用されているメトロポリスモンテカルロ法は、局所安定配置に捕まりやすく、そこでサンプリングが行き詰まる傾向があります。
 レプリカ交換法は、計算対象の系のコピー（レプリカ）を使って、この問題を克服することを目的としています。
 レプリカ交換法は、大まかに次のように説明できます（より正確な説明については、下記の文献を参照してください）。
@@ -75,7 +74,7 @@ 
                        8.1. レプリカ交換モンテカル
 
                      
 
                      
 
                      
-
                      8.2. ポピュレーションアニーリングモンテカルロ法
                      
+
                      8.2. ポピュレーションアニーリングモンテカルロ法
                      
 
                      基底状態を得るためのモンテカルロ法として、シミュレーテッドアニーリング (SA) 法が知られています。
 これは、温度一定のもとモンテカルロサンプリングを行い、一定のモンテカルロステップ数を実行した後に温度を強制的に下げていく手法です。
 はじめは高温での大域的な探索が行われ、シミュレーションが進むごとに低温化での局所安定配置の探索が行われます。
@@ -99,7 +98,7 @@ 
                      8.2. ポピュレーションアニー
 
                    
 
                    
 
                    
-
                    8.3. 配置と更新
                    
+
                    8.3. 配置と更新
                    
 
                    ここでは、 図 8.1 を例にabICSでの格子配置の定義とモンテカルロ法での更新の概要を説明します。
 (a)-(c)は unitcell 、 base_structure 、 defect_structure の概念図で、青丸、緑丸、黒丸はそれぞれ base_structure で定義される原子種、星印は defect_structure で定義される欠陥が入る位置を表します。
 (d)は  base_structure で原子種を指定する場合の概念図です。
@@ -118,7 +117,7 @@ 
                    8.3. 配置と更新
 ../_images/alg_sampling.png
 
                    
-
                    図 8.1 (a)-(e)abICSでの格子の定義と(f)モンテカルロ法の概要。詳細は本文に記載。
                    
+
                    図 8.1 (a)-(e)abICSでの格子の定義と(f)モンテカルロ法の概要。詳細は本文に記載。
                    
 
                    
 
 
                    
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diff --git a/docs/develop/ja/html/contact/index.html b/docs/develop/ja/html/contact/index.html
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     10. お問い合わせ — abICS 2.1-dev ドキュメント
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                    10. お問い合わせ
                    
 
                    abICS に関するお問い合わせはこちらにお寄せください。
                    
 
                      
 
                    • バグ報告
                      
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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     索引 — abICS 2.1-dev ドキュメント
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diff --git a/docs/develop/ja/html/how_to_use/index.html b/docs/develop/ja/html/how_to_use/index.html
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     3. 基本的な使用方法 — abICS 2.1-dev ドキュメント
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                    3. 基本的な使用方法
                    
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                    3. 基本的な使用方法
                    
 
                    
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                    3.1. 能動学習について
                    
+
                    3.1. 能動学習について
                    
 
                    abICSは元々、第一原理計算とレプリカ交換モンテカルロ法を直接組み合わせて統計熱力学計算を行うことを念頭に開発されましたが、
 計算できるモデル規模やステップ数が、第一原理計算の大きな計算コストのために限られてしまいます。
 これに対して、Ver. 2では、構造最適化後のエネルギーを高速に予測する機械学習モデルを構成するための能動学習手法を実装し、
@@ -54,7 +53,7 @@ 
                    3.1. 能動学習について
-
                    3.2. abICS制御用入力ファイルの準備
                    
+
                    3.2. abICS制御用入力ファイルの準備
                    
 
                    まず、abICSの動作全般を制御する入力ファイルを作成します。
 abICSの入力ファイルは, 以下の5つのセクションから構成されます.
                    
 
                      
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                      3.1. 能動学習について
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                      3.3. 第一原理ソルバー用参照ファイルの準備
                      
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                      3.3. 第一原理ソルバー用参照ファイルの準備
                      
 
                      訓練データの生成に用いる第一原理ソルバーの入力形式に従った入力ファイルを用意します。
 参照ファイルのパスはabICSの入力ファイルにある [mlref.solver] セクションの base_input_dir で指定します。
 座標情報については記載する必要はありません。
@@ -238,12 +237,12 @@ 
                      3.3. 第一原理ソルバー用参照
 
                  
 
                  
 
                  
-
                  3.3.1. 第一原理ソルバー利用時の注意点
                  
+
                  3.3.1. 第一原理ソルバー利用時の注意点
                  
 
                  原子座標以外の設定については基本的にソルバーごとに指定する必要があります。ただし、構造最適化をする原子の指定についてはabICS側で制御することが可能です。構造最適化機能を有効にする場合には、ソルバーの参照ファイルで構造最適化オプションを有効にした上で、構造最適化のステップ数なども指定することで最適化が行われます。
 また、abICSではソルバー毎に、参照ファイル名、実装時に仮定している参照ファイルのルールなどがあります。
 以下、それらについて説明します。
                  
 
                  
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                  VASP
                  
+
                  VASP
                  
 
                    
 
                  • URL : https://www.vasp.at
                    • 
 
                  • 参照ファイル
                    
@@ -259,7 +258,7 @@ 
                    VASP
-
                    Quantum Espresso
                    
+
                    Quantum Espresso
                    
 
                      
 
                    • URL : https://www.quantum-espresso.org
                      • 
 
                    • バージョンは 6.2 以上を利用してください。
                      
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                      Quantum Espresso
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                      OpenMX
                      
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                      OpenMX
                      
 
                        
 
                      • URL : http://www.openmx-square.org
                        • 
 
                      • バージョンは 3.9 を利用してください。
                        • 
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                        OpenMX
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                        3.4. 機械学習モデル訓練および評価用参照ファイルの準備
                        
+
                        3.4. 機械学習モデル訓練および評価用参照ファイルの準備
                        
 
                        使用する機械学習モデルソルバー（現在はaenetのみに対応）の入力形式に従った入力ファイルを用意します。
 参照ファイルのパスはabICSの入力ファイルにある [solver] セクションの base_input_dir で指定します。
 座標情報については、abICSの入力ファイルを参照するため、記載する必要はありません。
                        
 
                        
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                        3.4.1. 機械学習モデルソルバー利用時の注意点
                        
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                        3.4.1. 機械学習モデルソルバー利用時の注意点
                        
 
                        
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                        aenet
                        
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                        aenet
                        
 
                          
 
                        • URL : http://ann.atomistic.net
                          • 
 
                        • バージョン2.0.4 で動作確認済。
                          • 
@@ -325,21 +324,21 @@ 
                          aenet
-
                          3.5. 学習データの作成
                          
+
                          3.5. 学習データの作成
                          
 
                            
 
                          1. abics_mlref を用いて訓練データの大元となる第一原理計算用の入力ファイルを生成します。
                            2. 
 
                          2. 1で生成した入力ファイルに対して第一原理計算を実施します(チュートリアルでは GNU parallel を利用し網羅計算を実行しています)。
                            3. 
 
                          
 
                        
 
                        
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                        3.6. 機械学習モデルの作成
                        
+
                        3.6. 機械学習モデルの作成
                        
 
                          
 
                        1. abics_mlref を再度実行して、学習で用いる abics_train が読み込めるよう第一原理計算の結果を変換します。
                          2. 
 
                        2. 次に abics_train を実行して機械学習モデルの作成を行います。 計算が無事終了すると、 baseinput ディレクトリに学習済みの機械学習モデル（ニューラルネットワーク）が出力されます。
                          3. 
 
                        
 
                        
 
                        
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                        3.7. モンテカルロサンプリングの実行
                        
+
                        3.7. モンテカルロサンプリングの実行
                        
 
                        abics_sampling を用いてモンテカルロサンプリングを行います(MPI 実行時に指定するプロセス数はレプリカ数以上である必要があります)。
 実行すると、カレントディレクトリ以下にレプリカ番号を名前にもつディレクトリが作られ、各レプリカはその中でソルバーを実行します。
 なお、 LAMMPSインターフェースをもちいた aenet ライブラリ呼び込みにも対応しています(aenetPyLammps)。
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/index.html b/docs/develop/ja/html/index.html
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     Welcome to abICS's documentation! — abICS 2.1-dev ドキュメント
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                        Welcome to abICS's documentation!
                        
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                        Welcome to abICS's documentation!
                        
 
                        
-
                        Contents
                        
+
                        Contents
                        
 
                        
 
                          
 
                        • 1. abICS とは？
                            
@@ -109,7 +108,7 @@ 
                            Contents
-
                            Indices and tables
                            
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                            Indices and tables
                            
 
                              
 
                            • 索引
                              • 
 
                            • モジュール索引
                              • 
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diff --git a/docs/develop/ja/html/inputfiles/index.html b/docs/develop/ja/html/inputfiles/index.html
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     5. 入力ファイルフォーマット — abICS 2.1-dev ドキュメント
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                              5. 入力ファイルフォーマット
                              
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                              5. 入力ファイルフォーマット
                              
 
                              abICSの入力ファイルは, 以下の5つのセクションから構成されます.
                              
 
                                
 
                              1. [sampling] セクション
                                
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/inputfiles/parameter_config.html b/docs/develop/ja/html/inputfiles/parameter_config.html
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     5.6. [config] セクション — abICS 2.1-dev ドキュメント
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                                5.6. [config] セクション
                                
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                                5.6. [config] セクション
                                
 
                                多元系の原子配置やPotts 模型の格子サイズなど，配位に関するパラメータを指定します．
 以下のようなファイルフォーマットをしています．
                                
 
                                
@@ -87,14 +86,14 @@
 
                                
 
      
 
      
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      5.6.1. 入力形式
      
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      keyword = values の形式でキーワードとその値を指定します．
 また，#をつけることでコメントを入力することができます(それ以降の文字は無視されます)．
      
 
      
 
      
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      • 格子の指定
        
 
        
@@ -278,7 +277,7 @@ 
        solver.type
 
      
 
      
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      solver.type = "potts" の場合
      
 
      
 
        
 
      • Q
        
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/inputfiles/parameter_log.html b/docs/develop/ja/html/inputfiles/parameter_log.html
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     5.7. [log] セクション — abICS 2.1-dev ドキュメント
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        このセクションはログファイル名とログレベルを指定します。
        
 
        
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        keyword = values の形式でキーワードとその値を指定します.
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        • level
          
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diff --git a/docs/develop/ja/html/inputfiles/parameter_mlref.html b/docs/develop/ja/html/inputfiles/parameter_mlref.html
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     5.2. [mlref] セクション — abICS 2.1-dev ドキュメント
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          MC計算の結果から原子配置のみを取り出す際のオプションを設定します.
 例えばニューラルネットワークモデルの精度評価と訓練データの拡張などに利用します.
          
 
          以下のようなファイルフォーマットをしています.
          
@@ -47,12 +46,12 @@ 
          5.2. [mlref] セクション
-
          5.2.1. 入力形式
          
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          5.2.1. 入力形式
          
 
          keyword = value の形式でキーワードとその値を指定します.
 また, #をつけることでコメントを入力することができます(それ以降の文字は無視されます).
          
 
          
 
          
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          5.2.2. キーワード
          
+
          5.2.2. キーワード
          
 
            
 
          • レプリカに関する指定
            
 
            
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diff --git a/docs/develop/ja/html/inputfiles/parameter_observer.html b/docs/develop/ja/html/inputfiles/parameter_observer.html
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            計算する物理量を指定します.
 以下のようなファイルフォーマットをしています.
            
 
            
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            5.5. [observer] セクション
 
            
 
            
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            keyword = value の形式でキーワードとその値を指定します.
 また, #をつけることでコメントを入力することができます(それ以降の文字は無視されます).
            
 
            
 
            
-
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+
            5.5.2. キーワード
            
 
              
 
            • [[observer.solver]]
              
 
              物理量を計算するためのオプションを指定します.
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diff --git a/docs/develop/ja/html/inputfiles/parameter_sampling.html b/docs/develop/ja/html/inputfiles/parameter_sampling.html
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              レプリカ数や温度の幅, モンテカルロステップ数など,モンテカルロ部分のパラメータを指定します.
 以下のようなファイルフォーマットをしています.
              
 
              
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              5.1. [sampling] セクション
 
        
 
        
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        5.1.2. キーワード
        
 
          
 
        • サンプリング手法に関する指定
          
 
          
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          5.3. [sampling.solver], [mlref.solver] セクション
          
+
          5.3. [sampling.solver], [mlref.solver] セクション
          
 
          配位 (原子配置など) からエネルギーを計算するソルバーの設定を行います.
 sampling.solver はモンテカルロサンプリング中のエネルギー計算に,
 mlref.solver は機械学習モデルの訓練データ作成に使われます.
          
@@ -80,12 +79,12 @@ 
          5.3. [sampling.solver], [mlref.solver] 
 
          
 
      
 
      
-
      5.3.1. 入力形式
      
+
      5.3.1. 入力形式
      
 
      keyword = value の形式でキーワードとその値を指定します.
 また, #をつけることでコメントを入力することができます(それ以降の文字は無視されます).
      
 
      
 
      
-
      5.3.2. キーワード
      
+
      5.3.2. キーワード
      
 
        
 
      • type
        
 
        形式 : str型
        
@@ -262,7 +261,7 @@ 
        クイック検索
        
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/inputfiles/parameter_train.html b/docs/develop/ja/html/inputfiles/parameter_train.html
index d09f0d91..9f2fc01f 100644
--- a/docs/develop/ja/html/inputfiles/parameter_train.html
+++ b/docs/develop/ja/html/inputfiles/parameter_train.html
@@ -1,18 +1,17 @@
-
 
 
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     5.4. [train] セクション — abICS 2.1-dev ドキュメント
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        5.4. [train] セクション
        
+
        5.4. [train] セクション
        
 
        訓練データから配置エネルギー予測モデルを学習する学習器の設定を行います。
        
 
        予測モデルの作成・学習には外部のプログラムを利用します。
 現在はaenetのみに対応しています。
@@ -49,12 +48,12 @@ 
        5.4. [train] セクション
-
        5.4.1. 入力形式
        
+
        5.4.1. 入力形式
        
 
        keyword = value の形式でキーワードとその値を指定します.
 また, #をつけることでコメントを入力することができます(それ以降の文字は無視されます).
        
 
        
 
        
-
        5.4.2. キーワード
        
+
        5.4.2. キーワード
        
 
        
 
          
 
        • type
          
@@ -158,7 +157,7 @@ 
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/install/index.html b/docs/develop/ja/html/install/index.html
index 17477095..7e6d9d71 100644
--- a/docs/develop/ja/html/install/index.html
+++ b/docs/develop/ja/html/install/index.html
@@ -1,18 +1,17 @@
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+
   
     
     
 
     2. インストール方法 — abICS 2.1-dev ドキュメント
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          2. インストール方法
          
+
          2. インストール方法
          
 
          
 
            
 
          • 2.1. 必要なライブラリ・環境
            • 
@@ -121,7 +120,7 @@ 
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/install/install.html b/docs/develop/ja/html/install/install.html
index 7aac7fcb..4a888635 100644
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+++ b/docs/develop/ja/html/install/install.html
@@ -1,18 +1,17 @@
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     2.1. 必要なライブラリ・環境 — abICS 2.1-dev ドキュメント
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            2.1. 必要なライブラリ・環境
            
+
            2.1. 必要なライブラリ・環境
            
 
            abICS をインストール・実行するには、 バージョン3.7 以上の Python が必要です。
 また、以下の Python パッケージが必要です。
            
 
              
@@ -56,7 +55,7 @@ 
              2.1. 必要なライブラリ・環境
 
            
 
            
-
            2.2. PyPI からインストールする
            
+
            2.2. PyPI からインストールする
            
 
            abICS は PyPI に登録されているため、 pip コマンドで簡単にインストールできます。:
            
 
            $ pip3 install abics
 
            
@@ -69,15 +68,15 @@ 
            2.2. PyPI からインストールする
 
        
 
        
 
        
-
        2.3. ソースからインストールする
        
+
        2.3. ソースからインストールする
        
 
        多くの場合には PyPI からインストールすれば良いですが、機能追加する場合などはソースからインストールしてください。
        
 
        
-
        2.3.1. ダウンロード
        
+
        2.3.1. ダウンロード
        
 
        abICS のソースコードは GitHub page からダウンロードできます。
        
 
        $ git clone https://github.com/issp-center-dev/abICS
        
 
        
 
        
-
        2.3.2. ディレクトリ構成
        
+
        2.3.2. ディレクトリ構成
        
 
        abICSのディレクトリ構成は以下のようになっています.
 pythonモジュールは abics ディレクトリ以下に一式格納されています.
        
 
        .
@@ -102,7 +101,7 @@ 
        2.3.2. ディレクトリ構成
 
        
 
        
-
        2.3.3. インストール
        
+
        2.3.3. インストール
        
 
          
 
        • pip3 install の引数に abICS のルートディレクトリを渡すことでインストール可能です
          
 
          $ pip3 install ./abICS
@@ -113,7 +112,7 @@ 
          2.3.3. インストール
-
          2.4. アンインストール
          
+
          2.4. アンインストール
          
 
            
 
          • pip3 uninstall abics でアンインストールできます.
            • 
 
          
@@ -192,7 +191,7 @@ 
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/outputfiles/index.html b/docs/develop/ja/html/outputfiles/index.html
index 530e5136..66f9ac00 100644
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+++ b/docs/develop/ja/html/outputfiles/index.html
@@ -1,18 +1,17 @@
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     6. 出力ファイルフォーマット — abICS 2.1-dev ドキュメント
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          6. 出力ファイルフォーマット
          
+
          6. 出力ファイルフォーマット
          
 
          RANK はプロセス番号＝レプリカ番号を表します。
          
 
          
-
          6.1. RANK/structure.XXX.vasp
          
+
          6.1. RANK/structure.XXX.vasp
          
 
          各ステップごとの原子配置が VASP の POSCAR ファイル形式で出力されます。
 ステップ番号がファイル名の XXX に入ります。
          
 
          例:
          
@@ -59,11 +58,11 @@ 
          6.1. 
-
          6.2. RANK/minE.vasp
          
+
          6.2. RANK/minE.vasp
          
 
          最低エネルギーを与えた原子位置が VASP の POSCAR ファイル形式で出力されます。
          
 
          
 
          
-
          6.3. RANK/obs.dat
          
+
          6.3. RANK/obs.dat
          
 
          各ステップごとの温度とエネルギーが電子ボルト単位で出力されます。
          
 
          例:
          
 
          0      0.1034076       -41690.28269769395
@@ -75,7 +74,7 @@ 
          6.3. 
-
          6.4. RANK/obs_save.npy
          
+
          6.4. RANK/obs_save.npy
          
 
          各ステップごとのエネルギーが電子ボルト単位で出力されます。
 numpy.load('obs_save.npy') で、 darray として読み取ることができます。
          
 
          例:
          
@@ -89,7 +88,7 @@ 
          6.4. 
-
          6.5. RANK/kT_hist.npy
          
+
          6.5. RANK/kT_hist.npy
          
 
          各ステップごとの温度（電子ボルト単位）が Numpy バイナリ形式で出力されます。
 numpy.load('kT_hist.npy') で、 darray として読み取ることができます。
          
 
          例:
          
@@ -99,7 +98,7 @@ 
          6.5. 
-
          6.6. RANK/Trank_hist.npy
          
+
          6.6. RANK/Trank_hist.npy
          
 
          （RXMC のみ）
 各ステップごとの温度インデックスが Numpy バイナリ形式で出力されます。
 numpy.load('Trank_hist.npy') で、 darray として読み取ることができます。
          
@@ -110,7 +109,7 @@ 
          6.6. 
-
          6.7. RANK/logweight_hist.npy
          
+
          6.7. RANK/logweight_hist.npy
          
 
          (PAMC のみ)
 各ステップにおけるNeal-Jarzynski 重みの対数が Numpy バイナリ形式で出力されます。
          
 
          Example:
          
@@ -120,12 +119,12 @@ 
          6.7. 
-
          6.8. RANK/acceptance_ratio.dat
          
+
          6.8. RANK/acceptance_ratio.dat
          
 
          各温度におけるモンテカルロ更新の採択率。
 1列目に温度, 2列目に採択率（採択回数/更新回数）が出力されます。
          
 
          
 
          
-
          6.9. logZ.dat
          
+
          6.9. logZ.dat
          
 
          分配関数の対数 \(\log Z_i/Z_0\) (\(i\) は温度点の番号)。
          
 
            
 
          • 1列目は温度 \(T_i\)
            • 
@@ -134,7 +133,7 @@ 
            6.9. 
-
            6.10. <name>.dat
            
+
            6.10. <name>.dat
            
 
            温度ごとの物理量 \(O\) のカノニカル平均 \(\langle O \rangle\) とその統計誤差 \(\sigma[O]\) 。
 name は [[observer.solver]] の name キーワードで指定した名前です。
            
 
              
@@ -229,7 +228,7 @@ 
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/search.html b/docs/develop/ja/html/search.html
index 2ffafc09..a0108b94 100644
--- a/docs/develop/ja/html/search.html
+++ b/docs/develop/ja/html/search.html
@@ -1,18 +1,17 @@
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     検索 — abICS 2.1-dev ドキュメント
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              Related Topics
              
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/searchindex.js b/docs/develop/ja/html/searchindex.js
index 169a719c..4f7a63dd 100644
--- a/docs/develop/ja/html/searchindex.js
+++ b/docs/develop/ja/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["about/index", "about/info", "acknowledge/index", "algorithm/index", "contact/index", "how_to_use/index", "index", "inputfiles/index", "inputfiles/parameter_config", "inputfiles/parameter_log", "inputfiles/parameter_mlref", "inputfiles/parameter_observer", "inputfiles/parameter_sampling", "inputfiles/parameter_solver", "inputfiles/parameter_train", "install/index", "install/install", "outputfiles/index", "tools/index", "tools/tools_abicsRXsepT", "tools/tools_st2abics", "tutorial/aenet", "tutorial/index", "tutorial/qe", "tutorial/vasp"], "filenames": ["about/index.rst", "about/info.rst", "acknowledge/index.rst", "algorithm/index.rst", "contact/index.rst", "how_to_use/index.rst", "index.rst", "inputfiles/index.rst", "inputfiles/parameter_config.rst", "inputfiles/parameter_log.rst", "inputfiles/parameter_mlref.rst", "inputfiles/parameter_observer.rst", "inputfiles/parameter_sampling.rst", "inputfiles/parameter_solver.rst", "inputfiles/parameter_train.rst", "install/index.rst", "install/install.rst", "outputfiles/index.rst", "tools/index.rst", "tools/tools_abicsRXsepT.rst", "tools/tools_st2abics.rst", "tutorial/aenet.rst", "tutorial/index.rst", "tutorial/qe.rst", "tutorial/vasp.rst"], "titles": ["1. abICS \u3068\u306f\uff1f", "1.1. \u6982\u8981", "9. \u8b1d\u8f9e", "8. \u30a2\u30eb\u30b4\u30ea\u30ba\u30e0", "10. \u304a\u554f\u3044\u5408\u308f\u305b", "3. \u57fa\u672c\u7684\u306a\u4f7f\u7528\u65b9\u6cd5", "Welcome to abICS's documentation!", "5. \u5165\u529b\u30d5\u30a1\u30a4\u30eb\u30d5\u30a9\u30fc\u30de\u30c3\u30c8", "5.6. [config] \u30bb\u30af\u30b7\u30e7\u30f3", "5.7. [log] \u30bb\u30af\u30b7\u30e7\u30f3", "5.2. [mlref] \u30bb\u30af\u30b7\u30e7\u30f3", "5.5. [observer] \u30bb\u30af\u30b7\u30e7\u30f3", "5.1. [sampling] \u30bb\u30af\u30b7\u30e7\u30f3", "5.3. [sampling.solver], [mlref.solver] \u30bb\u30af\u30b7\u30e7\u30f3", "5.4. [train] \u30bb\u30af\u30b7\u30e7\u30f3", "2. \u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u65b9\u6cd5", "2.1. \u5fc5\u8981\u306a\u30e9\u30a4\u30d6\u30e9\u30ea\u30fb\u74b0\u5883", "6. \u51fa\u529b\u30d5\u30a1\u30a4\u30eb\u30d5\u30a9\u30fc\u30de\u30c3\u30c8", "7. \u4ed8\u5c5e\u30c4\u30fc\u30eb", "7.2. abicsRXsepT", "7.1. st2abics", "4.1. \u30cb\u30e5\u30fc\u30e9\u30eb\u30cd\u30c3\u30c8\u30ef\u30fc\u30af\u306e\u69cb\u7bc9", "4. \u30c1\u30e5\u30fc\u30c8\u30ea\u30a2\u30eb", "QuantumESPRESSO \u3092\u7528\u3044\u305f\u4f8b", "VASP \u3092\u7528\u3044\u305f\u4f8b"], "terms": {"\u6982\u8981": [0, 3, 6], "\u958b\u767a": [0, 2, 5, 6], "\u30d0\u30fc\u30b8\u30e7\u30f3": [0, 4, 5, 6, 16], "\u5c65\u6b74": [0, 6], "\u30e9\u30a4\u30bb\u30f3\u30b9": [0, 6, 24], "\u30b3\u30d4\u30fc\u30e9\u30a4\u30c8": [0, 6], "abics": [1, 2, 3, 4, 7, 14, 16, 18, 19, 20, 22], "\u7b2c\u4e00\u539f\u7406": [1, 6, 13, 21, 23], "\u8a08\u7b97": [1, 3, 5, 8, 10, 11, 12, 13, 14, 18, 19, 20, 22, 23, 24], "\u518d\u73fe": 1, "\u3059\u308b": [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24], "\u6a5f\u68b0": [1, 6, 13, 14, 21], "\u5b66\u7fd2": [1, 6, 7, 13, 14, 22], "\u30e2\u30c7\u30eb": [1, 6, 7, 13, 14], "\u8a13\u7df4": [1, 6, 7, 10, 13, 14, 21], "\u4e0d\u898f": 1, "\u5247\u7cfb": 1, "\u7d71\u8a08": [1, 5, 17], "\u71b1\u529b": [1, 5, 21], "\u30b5\u30f3\u30d7\u30ea\u30f3\u30b0": [1, 3, 5, 7, 12, 20, 22], "\u9ad8\u901f": [1, 5, 13, 21], "\u5b9f\u884c": [1, 3, 4, 6, 12, 13, 14, 16, 18, 19, 22], "\u305f\u3081": [1, 3, 4, 5, 7, 11, 12, 13, 14, 16, 18, 19, 20, 21, 23, 24], "\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u30d5\u30ec\u30fc\u30e0\u30ef\u30fc\u30af": 1, "\u3067\u3059": [1, 3, 5, 8, 9, 13, 16, 17, 19, 20, 21, 23, 24], "\u91d1\u5c5e": 1, "\u9178\u5316": 1, "\u7269\u5408": 1, "\u306a\u3069": [1, 4, 5, 7, 8, 10, 12, 13, 14, 16, 21, 23, 24], "\u591a\u6210": 1, "\u5206\u56fa": 1, "\u4f53\u7cfb": 1, "\u7279\u306b": 1, "\u91cd\u70b9": [1, 2], "\u7f6e\u3044": 1, "\u307e\u3059": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 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[[21, "id3"]], "abICS\u5236\u5fa1\u30d5\u30a1\u30a4\u30eb (input.toml)": [[21, "abics-input-toml"], [21, "id5"], [21, "id10"]], "(i)  [mlref] \u30bb\u30af\u30b7\u30e7\u30f3": [[21, "i-mlref"]], "(ii)  [mlref.solver] \u30bb\u30af\u30b7\u30e7\u30f3": [[21, "ii-mlref-solver"]], "(iii)  [config] \u30bb\u30af\u30b7\u30e7\u30f3": [[21, "iii-config"]], "QE\u53c2\u7167\u30d5\u30a1\u30a4\u30eb\u306e\u6e96\u5099": [[21, "qe"]], "\u30cb\u30e5\u30fc\u30e9\u30eb\u30cd\u30c3\u30c8\u30ef\u30fc\u30af\u751f\u6210\u7528\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u306e\u6e96\u5099": [[21, "id4"]], "(i)  [train] \u30bb\u30af\u30b7\u30e7\u30f3": [[21, "i-train"]], "aenet\u7528\u306e\u5165\u529b\u30d5\u30a1\u30a4\u30eb": [[21, "id6"]], "generate": [[21, "generate"]], "train": [[21, "train"]], "predict": [[21, "predict"]], "\u8a08\u7b97\u5b9f\u884c": [[21, "id7"], [21, "id11"]], "\u30e2\u30f3\u30c6\u30ab\u30eb\u30ed\u30b5\u30f3\u30d7\u30ea\u30f3\u30b0": [[21, "id8"]], "\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u306e\u6e96\u5099": [[21, "id9"]], "(i)  [sampling] \u30bb\u30af\u30b7\u30e7\u30f3": [[21, "i-sampling"]], "(ii)  [sampling.solver] \u30bb\u30af\u30b7\u30e7\u30f3": [[21, "ii-sampling-solver"]], "LAMMPS \u30a4\u30f3\u30bf\u30fc\u30d5\u30a7\u30fc\u30b9\u3092\u5229\u7528\u3057\u305f\u30b5\u30f3\u30d7\u30ea\u30f3\u30b0": [[21, "lammps"]], "aenet-lammps \u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb": [[21, "aenet-lammps"]], "\u30e2\u30c7\u30eb\u5b66\u7fd2": [[21, "id12"]], "\u30b5\u30f3\u30d7\u30ea\u30f3\u30b0": [[21, "id13"], [21, "id15"]], "predict \u7528\u5165\u529b\u30d5\u30a1\u30a4\u30eb": [[21, "id14"]], "\u30c1\u30e5\u30fc\u30c8\u30ea\u30a2\u30eb": [[22, "id1"]], "QuantumESPRESSO \u3092\u7528\u3044\u305f\u4f8b": [[23, "quantumespresso"]], "abICS \u306e\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u306e\u6e96\u5099": [[23, "abics"], [24, "abics"]], "QE \u306e\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u306e\u6e96\u5099": [[23, "qe"]], "\u5b9f\u884c\u30fb\u89e3\u6790": [[23, "id1"], [24, "id2"]], "VASP \u3092\u7528\u3044\u305f\u4f8b": [[24, "vasp"]], "VASP \u306e\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u306e\u6e96\u5099": [[24, "id1"]]}, "indexentries": {}})
\ No newline at end of file
diff --git a/docs/develop/ja/html/tools/index.html b/docs/develop/ja/html/tools/index.html
index 3addc547..a9644dd9 100644
--- a/docs/develop/ja/html/tools/index.html
+++ b/docs/develop/ja/html/tools/index.html
@@ -1,18 +1,17 @@
-
 
 
-
+
   
     
     
 
     7. 付属ツール — abICS 2.1-dev ドキュメント
-    
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@@ -34,7 +33,7 @@
           
          
             
   
          
-
          7. 付属ツール
          
+
          7. 付属ツール
          
 
          abICSには、典型的なワークフローを容易にするためのツールがいくつか付属しています。
          
 
            
 
          • 原子構造ファイルからabICS入力ファイルを作成するための st2abics
            • 
@@ -118,7 +117,7 @@ 
            クイック検索
            
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/ja/html/tools/tools_abicsRXsepT.html b/docs/develop/ja/html/tools/tools_abicsRXsepT.html
index 19892170..b7daec13 100644
--- a/docs/develop/ja/html/tools/tools_abicsRXsepT.html
+++ b/docs/develop/ja/html/tools/tools_abicsRXsepT.html
@@ -1,18 +1,17 @@
-
 
 
-
+
   
     
     
 
     7.2. abicsRXsepT — abICS 2.1-dev ドキュメント
-    
-    
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+    
+    
+    
+    
+    
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@@ -34,7 +33,7 @@
           
            
             
   
            
-
            7.2. abicsRXsepT
            
+
            7.2. abicsRXsepT
            
 
            このツールは、RXMC実行の各サンプリングステップで得られる構造とエネルギーを
 温度ごとに並べ替えるためのツールです。abICSのRXMC実行が終了した後に使用します:
            
 
            $ mpiexec -np NPROCS abicsRXsepT input.toml NSKIP
@@ -118,7 +117,7 @@ 
            クイック検索
            
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/ja/html/tools/tools_st2abics.html b/docs/develop/ja/html/tools/tools_st2abics.html
index c56332c2..561b6234 100644
--- a/docs/develop/ja/html/tools/tools_st2abics.html
+++ b/docs/develop/ja/html/tools/tools_st2abics.html
@@ -1,18 +1,17 @@
-
 
 
-
+
   
     
     
 
     7.1. st2abics — abICS 2.1-dev ドキュメント
-    
-    
-    
-    
-    
-    
+    
+    
+    
+    
+    
+    
     
     
     
@@ -35,7 +34,7 @@
           
            
             
   
            
-
            7.1. st2abics
            
+
            7.1. st2abics
            
 
            abICS 入力ファイル の [config]セクション を比較的簡単に作成するために、
 st2abics ツールを使うことができます。これはpymatgenで読める原子構造ファイルを読み取り、
 [config] セクションを埋めたabICS入力テンプレートファイルに変換します。元の構造ファイルからどのようにして
@@ -66,12 +65,12 @@ 
            7.1. [sampling], [mlref], [train], [observer] セクションのキーワードが空になっており、
 これらを記入した後、abICSの入力として使用することができます。
            
 
            
-
            7.1.1. 入力フォーマット
            
+
            7.1.1. 入力フォーマット
            
 
            st2abics の入力ファイルの例は、 examples/st2abics にあります(上の例では st2abics_CuZn.toml , st2abics_MgAl2O4.toml, st2abics_BZY.toml)。
            
 
            フォーマットはabICS入力ファイルの [config] セクションに似ています。
            
 
            
 
            
-
            7.1.2. キーワード
            
+
            7.1.2. キーワード
            
 
              
 
            • supercell
              
 
              形式 : list型
              
@@ -205,7 +204,7 @@ 
              クイック検索
              
       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
       |
-      Powered by Sphinx 6.2.1
+      Powered by Sphinx 7.2.5
       & Alabaster 0.7.13
       
       |
diff --git a/docs/develop/ja/html/tutorial/aenet.html b/docs/develop/ja/html/tutorial/aenet.html
index d90b8079..739818a1 100644
--- a/docs/develop/ja/html/tutorial/aenet.html
+++ b/docs/develop/ja/html/tutorial/aenet.html
@@ -1,18 +1,17 @@
-
 
 
-
+
   
     
     
 
     4.1. ニューラルネットワークの構築 — abICS 2.1-dev ドキュメント
-    
-    
-    
-    
-    
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+    
+    
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@@ -34,7 +33,7 @@
           
              
             
   
              
-
              4.1. ニューラルネットワークの構築
              
+
              4.1. ニューラルネットワークの構築
              
 
              ここでは、aenet を用いてニューラルネットワークモデルの構築を行う方法について記載します。
 第一原理ソルバーには Quantum ESPRESSO (QE) を使います。
 例題としてMgAl2O4スピネルのMg/Al反転度の温度依存性を計算します。
@@ -44,9 +43,9 @@
 以下では aenet および GNU parallel のインストールについても簡単に説明していますが、システムに既にインストールされている場合はそちらを使ってください。
 なお、計算の実行環境は物性研究所スーパーコンピュータシステムBのohtakaを利用しています。
              
 
              
-
              4.1.1. 事前準備
              
+
              4.1.1. 事前準備
              
 
              
-
              aenetのインストール
              
+
              aenetのインストール
              
 
              abICSでは、ニューラルネットワークモデルの構築のためにaenetを利用します。
 aenetは http://ann.atomistic.net からダウンロードできます。
 Documentation の Installation に従ってインストールしてください。
@@ -55,7 +54,7 @@ 
              aenetのインストール
-
              GNU parallelのインストール
              
+
              GNU parallelのインストール
              
 
              チュートリアルでは、GNU parallelを用いて Quantum Espresso による第一原理計算を並列実行します。
 GNU parallelは https://www.gnu.org/software/parallel/ からダウンロードできます (Macの場合はhomebrewにより直接インストールすることも可能です)。
 インストールは基本的には、ダウンロードして解凍したディレクトリ に移動した後、
              
@@ -66,7 +65,7 @@ 
              GNU parallelのインストール
 
              
 
              
-
              4.1.2. 学習データ生成用入力ファイルの準備
              
+
              4.1.2. 学習データ生成用入力ファイルの準備
              
 
              ニューラルネットワークの作成にあたり、
 原子配置を入力、エネルギーを出力とした学習データを、
 第一原理計算により作成する必要があります。
@@ -77,7 +76,7 @@ 
              4.1.2. 学習データ生成用入力フ
 
            
 
            に関する入力ファイルを準備する必要があります。
            
 
            
-
            abICS制御ファイル (input.toml)
            
+
            abICS制御ファイル (input.toml)
            
 
            計算対象とする格子構造の定義と、abICSによる能動学習のループ全体の制御、およびレプリカ交換モンテカルロ法に関するパラメータを設定します。
 st2abics ツールを使うことで、結晶構造ファイルから input.toml のひな形を自動で生成することができます。
            
 
            $ cd [example_dir]
@@ -86,7 +85,7 @@ 
            abICS制御ファイル (
 
            以下では input.toml の中で第一原理計算によ る学習データに関連するセクションの設定内容をもう少し詳しく解説します。
            
 
            
-
            (i)  [mlref] セクション
            
+
            (i)  [mlref] セクション
            
 
            [mlref]
 nreplicas = 8
 ndata = 5
@@ -98,7 +97,7 @@ 
            (i)  [mlref]
 
            
 
            
-
            (ii)  [mlref.solver] セクション
            
+
            (ii)  [mlref.solver] セクション
            
 
            [mlref.solver] # 参照第一原理ソルバーの設定
 type = 'qe'
 base_input_dir = ['./baseinput_ref', './baseinput_ref', './baseinput_ref'] #, './baseinput_ref']
@@ -121,7 +120,7 @@ 
            (ii)  [mlref.so
 モデルを使って訓練データを生成する場合は、無視する元素を指定します。
            
 
            
 
            
-
            (iii)  [config] セクション
            
+
            (iii)  [config] セクション
            
 
            [config] # 以下、結晶格子の情報と、格子上に配置される原子や空孔の情報が続く
 unitcell = [[8.1135997772, 0.0000000000, 0.0000000000],
             [0.0000000000, 8.1135997772, 0.0000000000],
@@ -147,7 +146,7 @@ 
            (iii)  [config]
 
            
 
            
 
            
-
            QE参照ファイルの準備
            
+
            QE参照ファイルの準備
            
 
            baseinput_ref にQEのscf計算で参照する入力ファイルを配置します。
 以下、サンプルディレクトリにある scf.in ファイルを記載します。
            
 
            &CONTROL
@@ -194,7 +193,7 @@ 
            QE参照ファイルの準備
-
            4.1.3. ニューラルネットワーク生成用入力ファイルの準備
            
+
            4.1.3. ニューラルネットワーク生成用入力ファイルの準備
            
 
            本チュートリアルではaenetを用いニューラルネットワークを作成します。
 ニューラルネットワークの作成には、
            
 
              
@@ -203,9 +202,9 @@ 
              4.1.3. ニューラルネットワーク
 
            
 
            に関する入力ファイルを準備・設定する必要があります。
            
 
            
-
            abICS制御ファイル (input.toml)
            
+
            abICS制御ファイル (input.toml)
            
 
            
-
            (i)  [train] セクション
            
+
            (i)  [train] セクション
            
 
            [train] # モデル学習器の設定
 type = 'aenet'
 base_input_dir = './aenet_train_input'
@@ -229,12 +228,12 @@ 
            (i)  [train]
 
            
 
            
-
            aenet用の入力ファイル
            
+
            aenet用の入力ファイル
            
 
            aenet用の入力ファイルを [train] セクションの base_input_dir で
 設定したディレクトリ内の generate 、 train 、および predict
 ディレクトリに設置します。
            
 
            
-
            generate
            
+
            generate
            
 
            aenetでは、訓練用の原子配置とエネルギーのデータを、原子環境記述子とエネルギーの関係に変換した中間バイナリフォーマットにまとめてから訓練を行います。
 この変換を行う generate.x 用の入力ファイルを generate ディレクトリに設置します。
            
 
            まず、原子種ごとの記述子設定ファイルを用意します。ファイル名は任意ですが、チュートリアルでは
@@ -281,7 +280,7 @@ 
            generategenerate.x を実行します。
            
 
            
 
            
-
            train
            
+
            train
            
 
            generate で生成された訓練データを読み込み、訓練を行う
 train.x 用の入力ファイルを train ディレクトリに設置します。
 ファイル名は train.in としてください：
            
@@ -310,7 +309,7 @@ 
            train
-
            predict
            
+
            predict
            
 
            訓練したポテンシャルモデルを使って入力座標に対してエネルギーを
 評価するための predict.x 用の入力ファイル predict.in を、 predict
 ディレクトリに設置します：
            
@@ -336,7 +335,7 @@ 
            predict
-
            計算実行
            
+
            計算実行
            
 
            入力ファイルの準備・設定が完了後、実際に計算する方法について説明します。
 サンプルスクリプトには、計算手順を簡略化するためのスクリプト  AL.sh が準備されています。
 run_pw.sh はQEの計算を実行するためのスクリプトで、後述する parallel_run.sh 内部で呼び出されます。
@@ -407,16 +406,16 @@ 
            計算実行
-
            4.2. モンテカルロサンプリング
            
+
            4.2. モンテカルロサンプリング
            
 
            次に、学習したニューラルネットワークポテンシャルを用い、abICSによりモンテカルロサンプリングをします。
            
 
            
-
            4.2.1. 入力ファイルの準備
            
+
            4.2.1. 入力ファイルの準備
            
 
            abICS でモンテカルロサンプリングを行うにはabICS制御ファイルでパラメータの設定をする必要があります。
            
 
            
-
            abICS制御ファイル (input.toml)
            
+
            abICS制御ファイル (input.toml)
            
 
            レプリカ交換モンテカルロ法に関連するセクション [sampling] で計算パラメータを設定します。
            
 
            
-
            (i)  [sampling] セクション
            
+
            (i)  [sampling] セクション
            
 
            [sampling]
 nreplicas = 8
 nprocs_per_replica = 1
@@ -436,7 +435,7 @@ 
            (i)  [sampling]
 基本的に、 nreplicas は [mlref] セクションと同じ値にしてください。
            
 
            
 
            
-
            (ii)  [sampling.solver] セクション
            
+
            (ii)  [sampling.solver] セクション
            
 
            [sampling.solver] # RXMC計算に使うソルバーの設定
 type = 'aenet'
 path= 'predict.x-2.0.4-ifort_serial'
@@ -459,7 +458,7 @@ 
            (ii)  [sampling
 
            
 
            
 
            
-
            4.2.2. 計算実行
            
+
            4.2.2. 計算実行
            
 
            サンプルスクリプトには、計算手順を簡略化するためのスクリプト  MC.sh が準備されています。
 MC.sh スクリプトの中身は以下の通りです。
            
 
            #!/bin/sh
@@ -506,12 +505,12 @@ 
            4.2.2. 計算実行
 
            
 
            
-
            4.2.3. LAMMPS インターフェースを利用したサンプリング
            
+
            4.2.3. LAMMPS インターフェースを利用したサンプリング
            
 
            モンテカルロサンプリングにおいては、 LAMMPSインターフェースをもちいた aenet ライブラリ呼び出しにも対応しています(aenetPyLammps ソルバー)。
 ファイル入出力などを行わないため、 aenet をプロセスとして呼び出すよりも高速に動作します。
 入力ファイル例としては examples/active_learning_qe_lammps を参考にしてください。
            
 
            
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            aenet-lammps のインストール
            
 
            aenetPyLammps の利用には、 aenet-lammps を組み込んだ LAMMPS のインストールが必要です。
            
 
            
 
            
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            モデル学習
            
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            モデル学習
            
 
            モデル学習のやりかたは前述の aenet によるものと同様です。
            
 
            
 
            
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            サンプリング
            
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            サンプリング
            
 
            
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            predict 用入力ファイル
            
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            predict 用入力ファイル
            
 
            predict.x でつかわれていた入力ファイル predict.in のかわりに、以下のような入力ファイル in.lammps を predict ディレクトリに設置してください:
            
 
            pair_style      aenet
 pair_coeff      * * v00 Al Mg 15t-15t.nn Al Mg
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            predict 用入力ファイルaenet-lammps リポジトリの README を参照してください。
            
 
            
 
            
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            サンプリング
            
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            サンプリング
            
 
            [sanmping.solver] セクションの type を 'aenetPyLammps' に、 run_scheme を 'function' に設定すると、 LAMMPS インターフェースを利用したサンプリングを実行できます。
            
 
            [sampling.solver]
 type = 'aenetPyLammps'
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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     4. チュートリアル — abICS 2.1-dev ドキュメント
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            このチュートリアルでは多元系イオン結晶 \({\rm Mg}{\rm Al}_2 {\rm O}_4\) の Mg, Al 原子の反転度計算を例に、abICSの利用方法について説明します。
 入力ファイルは examples/active_learning_qe/ にあります。
            
 
            
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/tutorial/qe.html b/docs/develop/ja/html/tutorial/qe.html
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     QuantumESPRESSO を用いた例 — abICS 2.1-dev ドキュメント
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            QuantumESPRESSO を用いた例
            
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            QuantumESPRESSO を用いた例
            
 
            
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            abICS の入力ファイルの準備
            
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            abICS の入力ファイルの準備
            
 
            abICS の入力ファイルは input_qe.toml です。
            
 
            [sampling]
 nreplicas = 2
@@ -161,7 +160,7 @@ 
            abICS の入力ファイルの準備Al 原子 16 個と、 Mg 原子 8 個を [[config.defect_structure]] で指定した座標中に動かします。
            
 
            
 
            
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            QE の入力ファイルの準備
            
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            QE の入力ファイルの準備
            
 
            abICS では、内部で保持した原子座標をもとに QE の入力ファイルを生成しますが、原子座標以外の情報、例えば擬ポテンシャルの情報は、ユーザが与える必要があります。
 QE の場合は、この情報は base_input_dir で指定したディレクトリの中に scf.in という名前で、 pw.x で使うファイルをそのまま置きます。
 このファイルをもとに、ユニットセルや原子座標などを書き換えた入力ファイルが自動生成されます。
            
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            QE の入力ファイルの準備
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            実行・解析
            
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            実行・解析
            
 
            MPI 実行におけるプロセス数やオプションの設定については 基本的な使用方法 を参照してください。
            
 
            mpiexec -np 2 abics_sampling input_qe.toml
 
            
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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diff --git a/docs/develop/ja/html/tutorial/vasp.html b/docs/develop/ja/html/tutorial/vasp.html
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     VASP を用いた例 — abICS 2.1-dev ドキュメント
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            abICS の入力ファイルの準備
            
 
            abICS の入力ファイルは input_vasp.toml です。
 以下、 examples/spinel にある input_vasp.toml を例に説明します。
 [sampling.solver] セクションのみ、QuantumESPRESSOと異なり、以下のように指定しています。
            
@@ -53,7 +52,7 @@ 
            abICS の入力ファイルの準備vasp を MPI_Comm_spawn で起動するため、 run_scheme として mpi_spawn_ready を与えます(VASPをソルバーとして利用する際には、MPI_COMM_SPAWNを利用するためのパッチをあてる必要があります。利用されたい場合には、お問い合わせ のその他に記載された連絡先までご連絡ください)。
            
 
            
 
            
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            VASP の入力ファイルの準備
            
 
            abICS では、内部で保持した原子座標をもとに VASP の入力ファイルを生成します。それ以外の情報は、ユーザが与える必要があります。
 この情報は base_input_dir で指定したディレクトリの中に INCAR 、 POSCAR 、 KPOINTS があります。
 上記のファイル以外にも、 POTCAR がVASPの実行には必要となりますが、ライセンスの関係上、サンプルファイルにはおいてありません。
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            VASP の入力ファイルの準備
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            実行・解析
            
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            実行・解析
            
 
            実行・解析の手順はQEの場合と同様です.
 QEの例と同じように、17 レプリカ、1000 ステップで計算をすると
            
 ../_images/doi_vasp.png
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       ©2019-, Institute for Solid State Physics, University of Tokyo.
       
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       & Alabaster 0.7.13
       
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